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Crystal structure of acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dgdp
Analyse Crystal structure of acanthamoeba polyphaga mimivirus nucleoside diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B6B
- Type
- protein
- Length
- 784 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
- DGI, MG
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 131 | 44% helix, 21% strand | Q5UQL3 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 129 | 45% helix, 20% strand | Q5UQL3 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 132 | 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
- DGI · 2'-deoxyguanosine-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
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 | 292 | 0.65 | 0.81 | 31 | empty |
| 2 | 286 | 0.63 | 0.81 | 34 | empty |
| 3 | 148 | 0.45 | 0.76 | 23 | MG, DGI |
| 4 | 116 | 0.44 | 0.78 | 21 | MG, DGI |
| 5 | 145 | 0.43 | 0.76 | 24 | MG, DGI |
Interfaces
6 interfaces between chains.
- B–F · 532 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 517 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 512 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 506 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3B6B · Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase… · the same entry in another collection · chain F against F, 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 3B6B · PDBe 3B6B · UniProt Q5UQL3
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