Research workbench
X-ray crystal structure of glutamine-dependent NAD+ synthetase from mycobacterium tuberculosis bound to naad+ and don
Analyse X-ray crystal structure of glutamine-dependent NAD+ synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DLA
- Type
- protein
- Length
- 2,614 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, ONL
- Pockets
- 20 · best druggability 0.84
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 | 651 | 43% helix, 18% strand | P0A5L6 |
| B | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 649 | 44% helix, 18% strand | P0A5L6 |
| C | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 657 | 43% helix, 17% strand | P0A5L6 |
| D | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 657 | 42% helix, 18% strand | P0A5L6 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 4 copies · chains A, D, B, C
- ONL · 5-oxo-L-norleucine · ligand · 4 copies · chains B, C, D, A
- GOL · Glycerol · additive · 15 copies · chains A, B, C, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.84 | 0.86 | 60 | ONL |
| 2 | 859 | 0.83 | 0.85 | 70 | ONL |
| 3 | 129 | 0.81 | 0.99 | 44 | empty |
| 4 | 99 | 0.77 | 0.98 | 28 | GOL |
| 5 | 628 | 0.71 | 0.79 | 60 | GOL |
Interfaces
5 interfaces between chains.
- B–D · 4042 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 1909 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1877 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1536 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1530 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3DLA · X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium… · 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 3DLA · PDBe 3DLA · UniProt P0A5L6
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