MolNFT v1 · #159129 · protein
Crystal structure of human glutamine-dependent NAD+ synthetase complexed with naad+, AMP, pyrophosphate, and MG2+
6OFB · Glutamine-dependent NAD(+) synthetase: “Crystal structure of human glutamine-dependent NAD+ synthetase complexed with naad+, AMP, pyrophosphate, and…”. X-ray diffraction, 5 ligands (DND, AMP, POP), 13 pockets (best druggability…
- PDB
- 6OFB
- Type
- protein
- Length
- 1,392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine-dependent NAD(+) synthetase
- EC
- 6.3.5.1
- UniProt
- Q6IA69
- Ligands
- DND, AMP, POP, MG, CL
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 696 | 44% helix, 17% strand | Q6IA69 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.84 | 0.85 | 91 | DND, AMP, POP, MG, CL |
| 2 | 1198 | 0.83 | 0.84 | 93 | DND, AMP, POP, MG, CL |
| 3 | 273 | 0.59 | 0.78 | 29 | empty |
| 4 | 258 | 0.57 | 0.78 | 28 | empty |
| 5 | 171 | 0.41 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4885 Ų buried · 81 hydrogen bonds · protein-protein
Compared structures
- 6OFB · Crystal structure of human glutamine-dependent NAD+ synthetase complexed with NaAD+, AMP… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6IA69 · AlphaFold monomer V2.0 prediction for glutamine-dependent NAD(+) synthetase (Q6IA69) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6IA69
- Elsewhere: RCSB PDB 6OFB · PDBe 6OFB · UniProt Q6IA69
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