MolNFT v1 · #143386 · protein
Crystal structure of a nucleoside diphosphate kinase ndk from helicobacter pylori
6AY1: “Crystal structure of a nucleoside diphosphate kinase ndk from helicobacter pylori”. X-ray diffraction. MolNFT v1 #143386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AY1
- Type
- protein
- Length
- 1,055 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- B5Z9W9
Structure
x-ray diffraction · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 138 | — | B5Z9W9 |
| B, C, D, H | — | protein | 137 | — | B5Z9W9 |
| E | — | protein | 134 | — | B5Z9W9 |
| F | — | protein | 106 | — | B5Z9W9 |
| G | — | protein | 129 | — | 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.
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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