MolNFT v1 · #140677 · protein
Crystal structure of tetrameric nucleoside diphosphate kinase at 1.98 a resolution from acinetobacter baumannii
5YIH: “Crystal structure of tetrameric nucleoside diphosphate kinase at 1.98 a resolution from acinetobacter…”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.82). MolNFT v1 #140677 on GenesisL1: 3D structure, binding…
- PDB
- 5YIH
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- D0CAF1
- Ligands
- MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 143 | 45% helix, 20% strand | D0CAF1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.82 | 0.83 | 94 | MG |
| 2 | 169 | 0.48 | 0.77 | 23 | empty |
| 3 | 201 | 0.47 | 0.75 | 24 | empty |
| 4 | 173 | 0.47 | 0.76 | 23 | empty |
| 5 | 169 | 0.46 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1263 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1252 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 412 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YIH · Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from… · 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 D0CAF1
- Elsewhere: RCSB PDB 5YIH · PDBe 5YIH · UniProt D0CAF1
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