2G82 | pdb_00002g82

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

PDB DOI: https://doi.org/10.2210/pdb2G82/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus aquaticus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-03-01 Released: 2007-03-13
Deposition Author(s): Jenkins, J.L., Buencamino, R., Tanner, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.172 (Depositor), 0.180 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

Jenkins, J.L., Buencamino, R., Tanner, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 293.66 kDa
Atom Count: 22,023
Modelled Residue Count: 2,640
Deposited Residue Count: 2,648
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth O] B [auth P] C [auth Q] D [auth R] E [auth A] A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	331	Thermus aquaticus	Mutation(s): 1 Gene Names: gap EC: 1.2.1.12
UniProt
Find proteins for P00361 (Thermus aquaticus) Explore P00361 Go to UniProtKB: P00361
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00361
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain I [auth O] SDF format, chain J [auth P] SDF format, chain N [auth R] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth D] SDF format, chain K [auth Q] SDF format, chain S [auth C] MOL2 format, chain I [auth O] MOL2 format, chain J [auth P] MOL2 format, chain N [auth R] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth D] MOL2 format, chain K [auth Q] MOL2 format, chain S [auth C] mmCIF format, chain I [auth O] mmCIF format, chain J [auth P] mmCIF format, chain N [auth R] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth D] mmCIF format, chain K [auth Q] mmCIF format, chain S [auth C]	I [auth O] J [auth P] K [auth Q] N [auth R] P [auth A] I [auth O], J [auth P], K [auth Q], N [auth R], P [auth A], Q [auth B], S [auth C], V [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth O] Focus chain J [auth P] Focus chain K [auth Q] Focus chain N [auth R] Focus chain P [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth O] Focus chain J [auth P] Focus chain K [auth Q] Focus chain N [auth R] Focus chain P [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain V [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C] mmCIF format, chain T [auth C]	T [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth Q] SDF format, chain O [auth R] SDF format, chain W [auth D] MOL2 format, chain M [auth Q] MOL2 format, chain O [auth R] MOL2 format, chain W [auth D] mmCIF format, chain M [auth Q] mmCIF format, chain O [auth R] mmCIF format, chain W [auth D]	M [auth Q], O [auth R], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth Q] Focus chain O [auth R] Focus chain W [auth D] Interactions & Density Focus chain M [auth Q] Focus chain O [auth R] Focus chain W [auth D]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain L [auth Q] SDF format, chain U [auth C] MOL2 format, chain L [auth Q] MOL2 format, chain U [auth C] mmCIF format, chain L [auth Q] mmCIF format, chain U [auth C]	L [auth Q], U [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain L [auth Q] Focus chain U [auth C] Interactions & Density Focus chain L [auth Q] Focus chain U [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A [auth O] B [auth P] C [auth Q] D [auth R] E [auth A] A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.172 (Depositor), 0.180 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.549	α = 90
b = 147.403	β = 90
c = 147.669	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-03-13

Deposition Author(s):

Jenkins, J.L.

Buencamino, R.

Tanner, J.J.

Revision History (Full details and data files)

Version 1.0: 2007-03-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Refinement description, Version format compliance
Version 1.3: 2014-11-12
Changes: Non-polymer description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary

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High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

2G82 | pdb_00002g82