MolNFT v1 · #63522 · protein
Crystal structure of the mimivirus ndk +kpn-N62L double mutant complexed with cdp
3FC9 · Nucleoside diphosphate kinase: “Crystal structure of the mimivirus ndk +kpn-N62L double mutant complexed with cdp”. X-ray diffraction, 3 ligands (CDP, CTP, MG), 8 pockets (best druggability 0.64). MolNFT v1 #63522 on GenesisL1: 3D…
- PDB
- 3FC9
- Type
- protein
- Length
- 800 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q5UQL3
- Ligands
- CDP, CTP, MG
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 134 | 44% helix, 19% strand | Q5UQL3 |
| B, C, E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 133 | 44% helix, 20% strand | Q5UQL3 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 5 copies · chains B, C, D, E, F
- CTP · Cytidine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.64 | 0.80 | 34 | empty |
| 2 | 302 | 0.63 | 0.80 | 32 | empty |
| 3 | 158 | 0.48 | 0.78 | 21 | MG, CDP |
| 4 | 148 | 0.48 | 0.78 | 21 | CTP |
| 5 | 133 | 0.47 | 0.78 | 21 | MG, CDP |
Interfaces
6 interfaces between chains.
- A–B · 582 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 580 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 579 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 573 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 571 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3FC9 · Crystal structure of the Mimivirus NDK +Kpn-N62L double mutant complexed with CDP · 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 3FC9 · PDBe 3FC9 · UniProt Q5UQL3
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