MolNFT v1 · #136871 · protein
Crystal structure of nucleoside diphosphate kinase from neisseria gonorrhoeae in complex with citrate
5V6D: “Crystal structure of nucleoside diphosphate kinase from neisseria gonorrhoeae in complex with citrate”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #136871 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V6D
- Type
- protein
- Length
- 2,245 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- B4RMG0
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, I, K | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 44% helix, 20% strand | B4RMG0 |
| C, E, O | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 139 | 44% helix, 19% strand | B4RMG0 |
| F, G, H, J, L, M, N, P | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 141 | 43% helix, 20% strand | B4RMG0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- CIT · Citric acid · additive · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.85 | 0.86 | 91 | empty |
| 2 | 1043 | 0.83 | 0.84 | 94 | empty |
| 3 | 1076 | 0.83 | 0.84 | 98 | empty |
| 4 | 374 | 0.72 | 0.84 | 66 | EDO |
| 5 | 707 | 0.72 | 0.79 | 77 | EDO |
Interfaces
36 interfaces between chains.
- K–L · 970 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 959 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 956 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 933 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5V6D · Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex… · the same entry in another collection · chain P against P, 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 B4RMG0
- Elsewhere: RCSB PDB 5V6D · PDBe 5V6D · UniProt B4RMG0
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