Download MendeleyCrystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcessus in complex with NADP
Abendroth, J., Dranow, D.M., Korotkov, K.V., Lorimer, D.D., Edwards, T.E.To be published.
4YMI | pdb_00004ymi
Crystal structure of probable nicotinate-nucleotide adenylyltransferase from Mycobacterium abcessus in complex with NADP
- PDB DOI: https://doi.org/10.2210/pdb4YMI/pdb
- Classification: TRANSFERASE
- Organism(s): Mycobacteroides abscessus ATCC 19977
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-03-06 Released: 2016-03-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.195 (Depositor), 0.190 (DCC)
- R-Value Work: 0.166 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.169 (Depositor)
Starting Model: experimental
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This is version 1.1 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 |
| Probable nicotinate-nucleotide adenylyltransferase | 233 | 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 | |
| NAP Query on NAP | C [auth A], F [auth B] | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N |  | ||
| ADE Query on ADE | D [auth A], E [auth A] | ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.195 (Depositor), 0.190 (DCC)
- R-Value Work: 0.166 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.169 (Depositor)
Diffraction Data: https://doi.org/10.18430/M34YMI
Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.29 | α = 90 |
| b = 115.24 | β = 90 |
| c = 56.76 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| ARP | model building |
| Coot | model building |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2016-03-09 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2016-03-09
Type: Initial release - Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
