Research workbench
PVHL:ELOB:ELOC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4- hydroxy-N-(4-(oxazol-5-YL)BENZYL)PYRROLIDINE-2-carboxamide (ligand 2)
Analyse PVHL:ELOB:ELOC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W9C
- Type
- protein
- Length
- 1,332 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription elongation factor B polypeptide 2; Transcription elongation factor B…
- UniProt
- Q15370, Q15369, P40337
- Ligands
- 3JG
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J | Transcription elongation factor B polypeptide 2 | protein | 103 | 15% helix, 39% strand | Q15370 |
| B | Transcription elongation factor B polypeptide 1 | protein | 86 | 49% helix, 15% strand | Q15369 |
| C | Von hippel-lindau disease tumor suppressor | protein | 141 | 24% helix, 30% strand | P40337 |
| D | Transcription elongation factor B polypeptide 2 | protein | 102 | 15% helix, 37% strand | Q15370 |
| E, H | Transcription elongation factor B polypeptide 1 | protein | 88 | 48% helix, 15% strand | Q15369 |
| F | Von hippel-lindau disease tumor suppressor | protein | 144 | 27% helix, 29% strand | P40337 |
| I, L | Von hippel-lindau disease tumor suppressor | protein | 143 | 25% helix, 29% strand | P40337 |
| K | Transcription elongation factor B polypeptide 1 | protein | 88 | 44% helix, 15% strand | Q15369 |
Ligands and binding sites
- 3JG · (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-oxazol-5-yl)benzyl]-L-prolinamide · ligand · 4 copies · chains C, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.61 | 0.79 | 40 | 3JG |
| 2 | 286 | 0.59 | 0.78 | 36 | 3JG |
| 3 | 132 | 0.44 | 0.76 | 30 | empty |
| 4 | 138 | 0.38 | 0.73 | 22 | empty |
| 5 | 135 | 0.37 | 0.73 | 24 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1156 Ų buried · 13 hydrogen bonds · protein-protein
- J–K · 1147 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1125 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1123 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1076 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (artifact).
Compared structures
- 4W9C · pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(oxazol-5-y… · the same entry in another collection · chain K against K, 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 4W9C · PDBe 4W9C · UniProt Q15370 · UniProt Q15369 · UniProt P40337
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