Research workbench
Crystal structure of the mimivirus ndk complexed with GDP
Analyse Crystal structure of the mimivirus ndk complexed with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GP9
- Type
- protein
- Length
- 788 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
- GDP, MG, PO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 133 | 44% helix, 21% strand | Q5UQL3 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 130 | 45% helix, 20% strand | Q5UQL3 |
| C, E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 132 | 44% helix, 21% strand | Q5UQL3 |
| D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 131 | 44% helix, 21% strand | Q5UQL3 |
| F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 130 | 45% helix, 22% strand | Q5UQL3 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, 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 | 299 | 0.63 | 0.80 | 30 | empty |
| 2 | 309 | 0.61 | 0.79 | 32 | empty |
| 3 | 138 | 0.46 | 0.78 | 21 | GDP, MG |
| 4 | 133 | 0.44 | 0.77 | 22 | GDP |
| 5 | 139 | 0.43 | 0.76 | 23 | GDP, PO4, MG |
Interfaces
6 interfaces between chains.
- B–D · 532 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 529 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 526 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 514 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3GP9 · Crystal structure of the Mimivirus NDK complexed with GDP · 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 3GP9 · PDBe 3GP9 · UniProt Q5UQL3
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