Research workbench
Crystal structure of M. tuberculosis glutamine-dependent NAD+ synthetase complexed with sulfonamide derivative 1, pyrophosphate, and glutamine
Analyse Crystal structure of M. tuberculosis glutamine-dependent NAD+ synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OFC
- Type
- protein
- Length
- 2,655 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine-dependent NAD(+) synthetase
- EC
- 6.3.5.1
- UniProt
- P9WJJ2
- Ligands
- SFH, GLN, POP, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 660 | 44% helix, 18% strand | P9WJJ2 |
| B | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 669 | 44% helix, 18% strand | P9WJJ2 |
| C | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 665 | 43% helix, 17% strand | P9WJJ2 |
| D | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 661 | 43% helix, 17% strand | P9WJJ2 |
Ligands and binding sites
- SFH · 5'-O-[(pyridine-3-carbonyl)sulfamoyl]adenosine · ligand · 8 copies · chains A, D, B, C
- GLN · Glutamine · ligand · 3 copies · chains B, D, C
- POP · Pyrophosphate 2- · ligand · chains B
- CL · Chloride ion · ion · 4 copies · chains A, D, B
- GOL · Glycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.84 | 0.85 | 75 | GLN |
| 2 | 878 | 0.84 | 0.86 | 67 | GLN |
| 3 | 151 | 0.82 | 0.98 | 40 | empty |
| 4 | 141 | 0.81 | 0.98 | 40 | empty |
| 5 | 971 | 0.80 | 0.81 | 84 | SFH, CL, POP |
Interfaces
5 interfaces between chains.
- B–D · 4030 Ų buried · 70 hydrogen bonds · protein-protein
- A–D · 1908 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1892 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1550 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1526 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6OFC · Crystal structure of M. tuberculosis glutamine-dependent NAD+ synthetase complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WJJ2 · AlphaFold monomer V2.0 prediction for glutamine-dependent NAD(+) synthetase (P9WJJ2) · a predicted model of the same protein · chain D against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P9WJJ2
- Elsewhere: RCSB PDB 6OFC · PDBe 6OFC · UniProt P9WJJ2
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