MolNFT v1 · #86108 · protein
PVHL:ELOB:ELOC complex, in complex with capped hydroxyproline
4AWJ · Transcription elongation factor B polypeptide 2: “PVHL:ELOB:ELOC complex, in complex with capped hydroxyproline”. X-ray diffraction, 1 ligand (V6F), 6 pockets (best druggability 0.59). MolNFT v1 #86108 on GenesisL1: 3D structure…
- PDB
- 4AWJ
- Type
- protein
- Length
- 1,320 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
- V6F
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 9 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription elongation factor B polypeptide 2 | protein | 102 | 15% helix, 37% strand | Q15370 |
| B, E | Transcription elongation factor B polypeptide 1 | protein | 87 | 48% helix, 15% strand | Q15369 |
| C | Von hippel-lindau disease tumor suppressor | protein | 136 | 19% helix, 32% strand | P40337 |
| D | Transcription elongation factor B polypeptide 2 | protein | 99 | 15% helix, 34% strand | Q15370 |
| F | Von hippel-lindau disease tumor suppressor | protein | 142 | 25% helix, 30% strand | P40337 |
| G, J | Transcription elongation factor B polypeptide 2 | protein | 103 | 17% helix, 39% strand | Q15370 |
| H | Transcription elongation factor B polypeptide 1 | protein | 87 | 45% helix, 15% strand | Q15369 |
| I, L | Von hippel-lindau disease tumor suppressor | protein | 144 | 24% helix, 30% strand | P40337 |
| K | Transcription elongation factor B polypeptide 1 | protein | 86 | 43% helix, 15% strand | Q15369 |
Ligands and binding sites
- V6F · (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide · ligand · 4 copies · chains C, F, I, L
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, E, F, H, I, K, L
- ACY · Acetic acid · additive · chains F
- GOL · Glycerol · additive · chains J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.59 | 0.79 | 36 | V6F |
| 2 | 218 | 0.57 | 0.79 | 39 | empty |
| 3 | 165 | 0.43 | 0.74 | 24 | empty |
| 4 | 155 | 0.42 | 0.74 | 28 | empty |
| 5 | 154 | 0.42 | 0.74 | 25 | empty |
Interfaces
15 interfaces between chains.
- G–H · 1157 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 1150 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1127 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1089 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1083 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (artifact).
Compared structures
- 4AWJ · pVHL:EloB:EloC complex, in complex with capped Hydroxyproline · the same entry in another collection · chain L against L, 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 4AWJ · PDBe 4AWJ · UniProt Q15370 · UniProt Q15369 · UniProt P40337
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