Download MendeleyMycobacterium abscessus NadD in complex with Mg-ATP, space group I41
Reed, R.W., Korotkov, K.V.To be published.
5DB4 | pdb_00005db4
Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41
- PDB DOI: https://doi.org/10.2210/pdb5DB4/pdb
- Classification: TRANSFERASE
- Organism(s): Mycobacteroides abscessus ATCC 19977
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-08-20 Released: 2016-08-24
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.28 Å
- R-Value Free: 0.248 (Depositor), 0.250 (DCC)
- R-Value Work: 0.193 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.196 (Depositor)
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nicotinate-nucleotide adenylyltransferase | 216 | Mycobacteroides abscessus ATCC 19977 | Mutation(s): 0 Gene Names: nadD, MAB_1621 EC: 2.7.7.18 |  | |
UniProt | |||||
Find proteins for B1MMZ4 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MMZ4 Go to UniProtKB: B1MMZ4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B1MMZ4 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | C [auth A], E [auth B] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| MG Query on MG | D [auth A], F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.28 Å
- R-Value Free: 0.248 (Depositor), 0.250 (DCC)
- R-Value Work: 0.193 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.196 (Depositor)
Space Group: I 41
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.098 | α = 90 |
| b = 67.098 | β = 90 |
| c = 229.538 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-08-24 Deposition Author(s): Reed, R.W., Korotkov, K.V., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R03AI117361 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P20GM103486 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P30GM110787 |
Revision History (Full details and data files)
- Version 1.0: 2016-08-24
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2019-12-11
Changes: Author supporting evidence - Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
