MolNFT v1 · #79309 · protein
Crystal structure of C176A glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPI and naad+
3SZG · Glutamine-dependent NAD(+) synthetase: “Crystal structure of C176A glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPI and naad+”. X-ray diffraction, 3 ligands (DND, AMP, POP), 20 pockets (best druggability…
- PDB
- 3SZG
- Type
- protein
- Length
- 2,617 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
- P0A5L6
- Ligands
- DND, AMP, POP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 650 | 43% helix, 18% strand | P0A5L6 |
| B | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 649 | 43% helix, 18% strand | P0A5L6 |
| C | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 660 | 43% helix, 18% strand | P0A5L6 |
| D | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 658 | 43% helix, 18% strand | P0A5L6 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 4 copies · chains A, D, B, C
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, D, C
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 | 848 | 0.83 | 0.85 | 69 | empty |
| 2 | 869 | 0.83 | 0.85 | 63 | empty |
| 3 | 140 | 0.81 | 0.98 | 42 | empty |
| 4 | 120 | 0.80 | 0.98 | 36 | GOL |
| 5 | 898 | 0.74 | 0.78 | 94 | DND, AMP, POP |
Interfaces
5 interfaces between chains.
- B–D · 4072 Ų buried · 69 hydrogen bonds · protein-protein
- A–D · 1943 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1935 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1519 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1514 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3SZG · Crystal structure of C176A glutamine-dependent NAD+ synthetase from M. tuberculosis bound… · the same entry in another collection · chain A 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 P0A5L6
- Elsewhere: RCSB PDB 3SZG · PDBe 3SZG · UniProt P0A5L6
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