MolNFT v2 · #218265 · protein
Crystal Structure of ligand ACBI3 in complex with KRAS G12D C118S GDP and pVHL:ElonginC:ElonginB complex
8QVU · Elongin-B: “Crystal Structure of ligand ACBI3 in complex with KRAS G12D C118S GDP and pVHL:ElonginC:ElonginB complex”. X-ray diffraction at 2.24, 4 ligands (WYL, GDP, MG), 10 pockets (best druggability 0.76). MolNFT v2 #218265 on…
- PDB
- 8QVU
- Type
- protein
- Length
- 986 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.24
- Source
- Homo sapiens
- Molecule
- Elongin-B; Elongin-C; von Hippel-Lindau disease tumor suppressor; Isoform 2B of GTPase…
- UniProt
- Q15370, Q15369, P40337, P01116
- Ligands
- WYL, GDP, MG, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.24 · 7 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Elongin-B | protein | 103 | 18% helix, 37% strand | Q15370 |
| G, C | Elongin-C | protein | 88 | 47% helix, 15% strand | Q15369 |
| F | von Hippel-Lindau disease tumor suppressor | protein | 144 | 24% helix, 31% strand | P40337 |
| D | Elongin-B | protein | 102 | 18% helix, 37% strand | Q15370 |
| B | von Hippel-Lindau disease tumor suppressor | protein | 147 | 24% helix, 29% strand | P40337 |
| E | Isoform 2B of GTPase KRas | protein | 159 | 35% helix, 23% strand | P01116 |
| A | Isoform 2B of GTPase KRas | protein | 155 | 37% helix, 12% strand | P01116 |
Ligands and binding sites
- WYL · (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 2 copies · chains B, A, F, E
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains E, A
- MG · Magnesium ion · metal · 2 copies · chains E, A
- PO4 · Phosphate ion · ion · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.76 | 0.81 | 55 | WYL |
| 2 | 1148 | 0.73 | 0.76 | 90 | WYL |
| 3 | 310 | 0.68 | 0.83 | 44 | GDP |
| 4 | 271 | 0.58 | 0.78 | 56 | GDP, MG |
| 5 | 232 | 0.58 | 0.79 | 25 | empty |
Interfaces
15 interfaces between chains.
- D–C · 1161 Ų buried · 14 hydrogen bonds · protein-protein
- H–G · 1149 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 1133 Ų buried · 15 hydrogen bonds · protein-protein
- G–F · 1106 Ų buried · 10 hydrogen bonds · protein-protein
- F–B · 829 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 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
- P40337 · AlphaFold monomer V2.0 prediction for von hippel-lindau disease tumor suppressor (P40337) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain C against A, TM-score 0.97
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
- Every structure of UniProt P01116
- Elsewhere: RCSB PDB 8QVU · PDBe 8QVU · UniProt Q15370 · UniProt Q15369 · UniProt P40337 · UniProt P01116
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