RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Gene Name = "ldtB"

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 40 Structures.

Refinements

Structure Determination Methodology

experimental (40)

Scientific Name of Source Organism

	Mycobacterium tuberculosis H37Rv (22)
	Mycobacterium tuberculosis (10)
	Mycobacterium tuberculosis CDC1551 (8)
	Corynebacterium jeikeium (2)

Taxonomy

Bacteria (40)

Experimental Method

X-RAY DIFFRACTION (40)

Polymer Entity Type

Protein (40)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (21)
	2.0 - 2.5 (17)
	2.5 - 3.0 (1)

Release Date

	2015 - 2019 (21)
	2020 - 2024 (19)

Enzyme Classification Name

Transferases (40)

Symmetry Type

	Asymmetric (40)
	Cyclic (7)

SCOP Classification

	All beta proteins (11)
	Artifacts (1)

AllSelected

1 to 25 of 40 Structures

Page 1 of 2

Sort by

Explore in 3D

4QR7 \| pdb_00004qr7	Download File View File

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Varughese, K.I.

To be published

Released	2015-07-29
Method	X-RAY DIFFRACTION 2.303 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,d-transpeptidase LdtB (protein)
Unique Ligands	DWZ, MLD

Explore in 3D

4QRA \| pdb_00004qra	Download File View File

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Varughese, K.I.

To be published

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,d-transpeptidase LdtB (protein)
Unique Ligands	CA

Explore in 3D

4QRB \| pdb_00004qrb	Download File View File

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Varughese, K.I.

To be published

Released	2015-12-23
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,d-transpeptidase LdtB (protein)
Unique Ligands	MLD

Explore in 3D

4QTF \| pdb_00004qtf	Download File View File

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Varughese, K.I.

To be published

Released	2015-07-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,d-transpeptidase LdtB (protein)
Unique Ligands	3V5, MLD

Explore in 3D

5D7H \| pdb_00005d7h	Download File View File

X-RAY CRYSTAL STRUCTURE OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

Saavedra, H., Basta, L.A., Lamichhane, G., Bianchet, M.A.

(2017) BMC Biochem 18: 8-8

Released	2016-09-28
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	GOL, SO4

Explore in 3D

5DC2 \| pdb_00005dc2	Download File View File

X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

Pan, Y., Basta, L., Lamichhane, G., Bianchet, M.A.

(2017) BMC Biochem 18: 8-8

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.182 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	58U, EDO, GOL, PEG, PGE, SO4

Explore in 3D

5DCC \| pdb_00005dcc	Download File View File

X-RAY CRYSTAL STRUCTURE OF a TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

Pan, Y., Basta, L., Lamichhane, G., Bianchet, M.A.

(2017) BMC Biochem 18: 8-8

Released	2016-09-28
Method	X-RAY DIFFRACTION 2.451 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	58U, EDO, GOL, PEG, PGE, SO4

Explore in 3D

5DU7 \| pdb_00005du7	Download File View File

Crystal structure of ldtMt2 at 1.79 Angstrom resolution

Kumar, P., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-09-28
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)

Explore in 3D

5DUJ \| pdb_00005duj	Download File View File

Crystal structure of ldtMt2 in complex with Faropenem adduct

Kumar, P., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-09-28
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	BME, DGF, SO4

Explore in 3D

5DVP \| pdb_00005dvp	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct

Kumar, P., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-09-28
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	DRW, POA, SO4

Explore in 3D

5DZJ \| pdb_00005dzj	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation A

Kumar, P., Ginell, S.L., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.095 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6B7

Explore in 3D

5DZP \| pdb_00005dzp	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation B

Kumar, P., Ginell, S.L., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6B7

Explore in 3D

5E1G \| pdb_00005e1g	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208

Kumar, P., Lamichhane, G., Ginell, S.L.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-12
Method	X-RAY DIFFRACTION 1.852 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	T8G

Explore in 3D

5E1I \| pdb_00005e1i	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210

Kumar, P., Ginell, S.L., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-12
Method	X-RAY DIFFRACTION 2.003 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6B8, GOL, NA

Explore in 3D

5K69 \| pdb_00005k69	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224

Lamichhane, G., Ginell, S.L., Kumar, P.

(2017) Nat Chem Biol 13: 54-61

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6QR, GOL

Explore in 3D

5LB1 \| pdb_00005lb1	Download File View File

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with thionitrobenzoate (TNB) adduct at the active site cysteine-354

Steiner, E.M., Schnell, R., Schneider, G.

(2017) FEBS J 284: 725-741

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	MNB

Explore in 3D

5LBG \| pdb_00005lbg	Download File View File

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with faropenem-derived adduct at the active site cysteine-354

Steiner, E.M., Schnell, R., Schneider, G.

(2017) FEBS J 284: 725-741

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	3HL

Explore in 3D

6IYV \| pdb_00006iyv	Download File View File

Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with ertapenem adduct

Zhao, F., Li, D.F., Wang, D.C.

(2019) Biochem Biophys Res Commun 510: 254-260

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	2RG, GOL, PEG, SO4, TRS

Explore in 3D

6IYW \| pdb_00006iyw	Download File View File

Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with Imipenem adduct

Li, D.F., Zhao, F., Wang, D.C.

(2019) Biochem Biophys Res Commun 510: 254-260

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	GOL, IM2

Explore in 3D

6LQB \| pdb_00006lqb	Download File View File

A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct

Li, D.F., Qin, Y.L.

(2020) PROG BIOCHEM BIOPHYS 47: 989-997

Released	2021-01-13
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	2RG, ACY, GOL

Explore in 3D

6RLG \| pdb_00006rlg	Download File View File

Crystal structure of LdtMt2 from Mycobacterium tuberculosis

Brem, J., Lohans, C., Schofield, C.

(2019) Chem Commun (Camb) 55: 10214-10217

Released	2019-08-14
Method	X-RAY DIFFRACTION 1.51000183032 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	EDO, NA, NO3, TRS

Explore in 3D

6RRM \| pdb_00006rrm	Download File View File

Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen

Brem, J., Lohans, C., Schofield, C.

(2019) Chem Commun (Camb) 55: 10214-10217

Released	2019-08-14
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Mycobacterium tuberculosis CDC1551
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	9JT, EDO, GOL, NH4

Explore in 3D

7A0Z \| pdb_00007a0z	Download File View File

LppS with covalent adduct derived from 1b

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	BT6, TAM

Explore in 3D

7A10 \| pdb_00007a10	Download File View File

LppS with covalent adduct derived from 1g

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	QU5

Explore in 3D

7A11 \| pdb_00007a11	Download File View File

LppS with covalent adduct derived from 1E

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	ACT, XL3

1 to 25 of 40 Structures

Page 1 of 2

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

4QR7 | pdb_00004qr7

4QRA | pdb_00004qra

4QRB | pdb_00004qrb

4QTF | pdb_00004qtf

5D7H | pdb_00005d7h

5DC2 | pdb_00005dc2

5DCC | pdb_00005dcc

5DU7 | pdb_00005du7

5DUJ | pdb_00005duj

5DVP | pdb_00005dvp

5DZJ | pdb_00005dzj

5DZP | pdb_00005dzp

5E1G | pdb_00005e1g

5E1I | pdb_00005e1i

5K69 | pdb_00005k69

5LB1 | pdb_00005lb1

5LBG | pdb_00005lbg

6IYV | pdb_00006iyv

6IYW | pdb_00006iyw

6LQB | pdb_00006lqb

6RLG | pdb_00006rlg

6RRM | pdb_00006rrm

7A0Z | pdb_00007a0z

7A10 | pdb_00007a10

7A11 | pdb_00007a11