MolNFT v1 · #124508 · protein
Structure of glutamine-dependent NAD+ synthetase from acinetobacter baumannii in complex with adenosine diphosphate (ADP)
5KHA: “Structure of glutamine-dependent NAD+ synthetase from acinetobacter baumannii in complex with adenosine…”. X-ray diffraction, 2 ligands (ADP, CL), 10 pockets (best druggability 0.86). MolNFT v1 #124508 on GenesisL1: 3D structure…
- PDB
- 5KHA
- Type
- protein
- Length
- 1,052 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, 6.3.1.5
- UniProt
- V5VHL3
- Ligands
- ADP, CL
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine-dependent NAD+ synthetase (EC 6.3.5.1, 6.3.1.5) | protein | 526 | 40% helix, 20% strand | V5VHL3 |
| B | Glutamine-dependent NAD+ synthetase (EC 6.3.5.1, 6.3.1.5) | protein | 526 | 40% helix, 20% strand | V5VHL3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.86 | 0.87 | 111 | EDO |
| 2 | 398 | 0.62 | 0.78 | 53 | ADP |
| 3 | 296 | 0.62 | 0.79 | 39 | empty |
| 4 | 300 | 0.58 | 0.78 | 49 | ADP |
| 5 | 168 | 0.47 | 0.76 | 28 | CL |
Interfaces
1 interface between chains.
- A–B · 5314 Ų buried · 99 hydrogen bonds · protein-protein
Compared structures
- 5KHA · Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex… · 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 V5VHL3
- Elsewhere: RCSB PDB 5KHA · PDBe 5KHA · UniProt V5VHL3
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