Research workbench
Crystal structure of sivrcm vif-cbfbeta-elob-eloc complex
Analyse Crystal structure of sivrcm vif-cbfbeta-elob-eloc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P59
- Type
- protein
- Length
- 1,087 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core-binding factor subunit beta; Elongin-B; Elongin-C; Virion infectivity factor
- UniProt
- Q13951, Q15370, Q15369, E1ANT9
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Core-binding factor subunit beta | protein | 155 | 26% helix, 32% strand | Q13951 |
| W, D | Elongin-B | protein | 98 | 19% helix, 33% strand | Q15370 |
| Z, E | Elongin-C | protein | 96 | 43% helix, 14% strand | Q15369 |
| F | Virion infectivity factor | protein | 191 | 29% helix, 25% strand | E1ANT9 |
| A | Core-binding factor subunit beta | protein | 157 | 25% helix, 31% strand | Q13951 |
| B | Virion infectivity factor | protein | 196 | 28% helix, 24% strand | E1ANT9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains F, B
- GOL · Glycerol · additive · 2 copies · chains F, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.67 | 0.79 | 55 | empty |
| 2 | 279 | 0.63 | 0.81 | 38 | empty |
| 3 | 228 | 0.58 | 0.80 | 44 | empty |
| 4 | 280 | 0.54 | 0.76 | 29 | GOL |
| 5 | 233 | 0.50 | 0.75 | 28 | GOL |
Interfaces
9 interfaces between chains.
- C–F · 3282 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3185 Ų buried · 54 hydrogen bonds · protein-protein
- W–Z · 1106 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1078 Ų buried · 16 hydrogen bonds · protein-protein
- E–B · 921 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6P59 · Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain E against A, TM-score 0.91
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 Q13951
- Every structure of UniProt Q15370
- Every structure of UniProt Q15369
- Every structure of UniProt E1ANT9
- Elsewhere: RCSB PDB 6P59 · PDBe 6P59 · UniProt Q13951 · UniProt Q15370 · UniProt Q15369 · UniProt E1ANT9
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