MolNFT v1 · #62977 · protein
Crystal structure of the mimivirus ndk +kpn-N62L-R107G triple mutant complexed with dcdp
3EVM · Nucleoside diphosphate kinase: “Crystal structure of the mimivirus ndk +kpn-N62L-R107G triple mutant complexed with dcdp”. X-ray diffraction, 2 ligands (YYY, MG), 4 pockets (best druggability 0.50). MolNFT v1 #62977 on GenesisL1: 3D…
- PDB
- 3EVM
- Type
- protein
- Length
- 267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q5UQL3
- Ligands
- YYY, MG
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 134 | 43% helix, 19% strand | Q5UQL3 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 133 | 44% helix, 20% strand | Q5UQL3 |
Ligands and binding sites
- YYY · Deoxycytidine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.50 | 0.86 | 18 | empty |
| 2 | 172 | 0.48 | 0.76 | 28 | YYY, MG |
| 3 | 144 | 0.46 | 0.77 | 24 | YYY, MG |
| 4 | 58 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3EVM · Crystal structure of the Mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with dCDP · 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 Q5UQL3
- Elsewhere: RCSB PDB 3EVM · PDBe 3EVM · UniProt Q5UQL3
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