MolNFT v1 · #122417 · protein
Crystal structure of nucleoside diphosphate kinase from schistosoma mansoni
5IOL: “Crystal structure of nucleoside diphosphate kinase from schistosoma mansoni”. X-ray diffraction, 16 pockets (best druggability 0.87). MolNFT v1 #122417 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IOL
- Type
- protein
- Length
- 1,792 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- G4VJY9
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, G, I, J, K | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 149 | 46% helix, 17% strand | G4VJY9 |
| D, F, H, L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 45% helix, 17% strand | G4VJY9 |
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.87 | 0.89 | 109 | empty |
| 2 | 269 | 0.80 | 0.92 | 40 | empty |
| 3 | 267 | 0.80 | 0.92 | 40 | empty |
| 4 | 270 | 0.80 | 0.92 | 39 | empty |
| 5 | 312 | 0.80 | 0.90 | 40 | empty |
Interfaces
27 interfaces between chains.
- A–C · 1051 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1049 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1048 Ų buried · 15 hydrogen bonds · protein-protein
- E–K · 1045 Ų buried · 20 hydrogen bonds · protein-protein
- D–H · 1045 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5IOL · Crystal structure of Nucleoside Diphosphate Kinase from Schistosoma mansoni · 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 G4VJY9
- Elsewhere: RCSB PDB 5IOL · PDBe 5IOL · UniProt G4VJY9
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