Research workbench
Structure of pvhl-elongin B-elongin C (vcb) in complex with hydroxylated-hif-2ALPHA (523-542) in the C2221 form
Analyse Structure of pvhl-elongin B-elongin C (vcb) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I7Q
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongin-B; Elongin-C; Endothelial pas domain-containing protein 1; Von hippel-lindau…
- UniProt
- Q15370, Q2KII4, Q99814, P40337
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Elongin-B | protein | 105 | 17% helix, 38% strand | Q15370 |
| C | Elongin-C | protein | 97 | 42% helix, 13% strand | Q2KII4 |
| H | Endothelial pas domain-containing protein 1 | protein | 17 | 0% helix, 18% strand | Q99814 |
| V | Von hippel-lindau disease tumor suppressor | protein | 151 | 27% helix, 30% strand | P40337 |
Ligands and binding sites
- GOL · Glycerol · additive · chains C, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.44 | 0.78 | 20 | empty |
| 2 | 52 | 0.24 | 0.71 | 12 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1150 Ų buried · 16 hydrogen bonds · protein-protein
- C–V · 1052 Ų buried · 14 hydrogen bonds · protein-protein
- H–V · 909 Ų buried · 16 hydrogen bonds · protein-protein
- B–V · 199 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (disulfide, hydroxylation, oxidation).
Compared structures
- 6I7Q · Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha… · 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 B against A, TM-score 0.98
- Q2KII4 · AlphaFold monomer V2.0 prediction for elongin-C (Q2KII4) · a predicted model of the same protein · chain C against A, TM-score 0.91
- Q99814 · AlphaFold monomer V2.0 prediction for endothelial pas domain- containing protein 1… · a predicted model of the same protein · chain H against A, TM-score 0.25
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 Q15370
- Every structure of UniProt Q2KII4
- Every structure of UniProt Q99814
- Every structure of UniProt P40337
- Elsewhere: RCSB PDB 6I7Q · PDBe 6I7Q · UniProt Q15370 · UniProt Q2KII4 · UniProt Q99814 · UniProt P40337
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