MolNFT v1 · #150211 · protein
PVHL:ELOB:ELOC in complex with 6-chlorothiochroman-4-one
6GMX · Elongin-B: “PVHL:ELOB:ELOC in complex with 6-chlorothiochroman-4-one”. X-ray diffraction, 1 ligand (F7B), 11 pockets (best druggability 0.59). MolNFT v1 #150211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GMX
- Type
- protein
- Length
- 1,318 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongin-B; Elongin-C; Von hippel-lindau disease tumor suppressor
- UniProt
- Q15370, Q15369, P40337
- Ligands
- F7B
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J | Elongin-B | protein | 103 | 15% helix, 37% strand | Q15370 |
| B, E | Elongin-C | protein | 87 | 48% helix, 15% strand | Q15369 |
| C | Von hippel-lindau disease tumor suppressor | protein | 138 | 22% helix, 30% strand | P40337 |
| D | Elongin-B | protein | 96 | 20% helix, 35% strand | Q15370 |
| F | Von hippel-lindau disease tumor suppressor | protein | 142 | 26% helix, 30% strand | P40337 |
| H | Elongin-C | protein | 85 | 47% helix, 15% strand | Q15369 |
| I, L | Von hippel-lindau disease tumor suppressor | protein | 144 | 25% helix, 29% strand | P40337 |
| K | Elongin-C | protein | 86 | 47% helix, 15% strand | Q15369 |
Ligands and binding sites
- F7B · 6-chloranyl-2,3-dihydrothiochromen-4-one · ligand · 2 copies · chains B, K
- IPA · Isopropyl alcohol · additive · 4 copies · chains C, F, I, L
- ACT · Acetate ion · additive · 2 copies · chains E, F, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.59 | 0.79 | 31 | F7B |
| 2 | 202 | 0.52 | 0.77 | 27 | empty |
| 3 | 50 | 0.50 | 0.87 | 14 | empty |
| 4 | 169 | 0.49 | 0.77 | 30 | empty |
| 5 | 145 | 0.42 | 0.75 | 20 | empty |
Interfaces
17 interfaces between chains.
- J–K · 1140 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1134 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1116 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1086 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1071 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (artifact).
Compared structures
- 6GMX · pVHL:EloB:EloC in complex with 6-chlorothiochroman-4-one · the same entry in another collection · chain H against H, 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 Q15370
- Every structure of UniProt Q15369
- Every structure of UniProt P40337
- Elsewhere: RCSB PDB 6GMX · PDBe 6GMX · UniProt Q15370 · UniProt Q15369 · UniProt P40337
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