Research workbench
Crystal structure of a nucleoside diphosphate kinase ndk from helicobacter pylori
Analyse Crystal structure of a nucleoside diphosphate kinase ndk from helicobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AY1
- Type
- protein
- Length
- 1,055 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- B5Z9W9
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 138 | 46% helix, 20% strand | B5Z9W9 |
| B, C, D, H | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 137 | 47% helix, 20% strand | B5Z9W9 |
| E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 134 | 45% helix, 19% strand | B5Z9W9 |
| F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 106 | 46% helix, 22% strand | B5Z9W9 |
| G | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 129 | 46% helix, 22% strand | B5Z9W9 |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, D
- HEZ · Hexane-1,6-diol · additive · 2 copies · chains C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.79 | 0.81 | 66 | empty |
| 2 | 1036 | 0.79 | 0.81 | 71 | empty |
| 3 | 59 | 0.66 | 0.94 | 26 | empty |
| 4 | 384 | 0.58 | 0.75 | 51 | MPD |
| 5 | 158 | 0.57 | 0.82 | 27 | empty |
Interfaces
15 interfaces between chains.
- C–D · 821 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 820 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 776 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 697 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6AY1 · Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori · the same entry in another collection · chain H against H, TM-score 1.00
- B5Z9W9 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (B5Z9W9) · a predicted model of the same protein · chain G 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 B5Z9W9
- Elsewhere: RCSB PDB 6AY1 · PDBe 6AY1 · UniProt B5Z9W9
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