MolNFT v1 · #84764 · protein
PVHL54-213-elob-eloc COMPLEX_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-YL)ACETYL)-N-(4-NITROBENZYL)PYRROLIDINE-2-carboxamide bound
3ZUN · Transcription elongation factor B polypeptide 2: “PVHL54-213-elob-eloc COMPLEX_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol…”. X-ray diffraction, 1 ligand (ZUN), 8 pockets (best druggability 0.57). MolNFT v1 #84764 on GenesisL1: 3D…
- PDB
- 3ZUN
- Type
- protein
- Length
- 1,319 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
- ZUN
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 10 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription elongation factor B polypeptide 2 | protein | 102 | 19% helix, 35% strand | Q15370 |
| B, K | Transcription elongation factor B polypeptide 1 | protein | 86 | 48% helix, 15% strand | Q15369 |
| C | Von hippel-lindau disease tumor suppressor | protein | 137 | 23% helix, 29% strand | P40337 |
| D | Transcription elongation factor B polypeptide 2 | protein | 101 | 19% helix, 32% strand | Q15370 |
| E, H | Transcription elongation factor B polypeptide 1 | protein | 87 | 47% helix, 15% strand | Q15369 |
| F | Von hippel-lindau disease tumor suppressor | protein | 143 | 24% helix, 29% strand | P40337 |
| G | Transcription elongation factor B polypeptide 2 | protein | 103 | 14% helix, 37% strand | Q15370 |
| I | Von hippel-lindau disease tumor suppressor | protein | 144 | 26% helix, 29% strand | P40337 |
| J | Transcription elongation factor B polypeptide 2 | protein | 104 | 15% helix, 37% strand | Q15370 |
| L | Von hippel-lindau disease tumor suppressor | protein | 139 | 22% helix, 30% strand | P40337 |
Ligands and binding sites
- ZUN · (4R)-N-[4-(dihydroxyamino)benzyl]-4-hydroxy-1-[(3-methylisoxazol-5-yl)acetyl]-L-prolinamide · ligand · 4 copies · chains C, F, I, L
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.57 | 0.77 | 32 | ZUN |
| 2 | 228 | 0.55 | 0.77 | 37 | ZUN |
| 3 | 88 | 0.48 | 0.82 | 19 | empty |
| 4 | 52 | 0.43 | 0.83 | 17 | empty |
| 5 | 155 | 0.42 | 0.74 | 23 | empty |
Interfaces
17 interfaces between chains.
- G–H · 1115 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1103 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1098 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 1086 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1075 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3ZUN · pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol… · 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 3ZUN · PDBe 3ZUN · UniProt Q15370 · UniProt Q15369 · UniProt P40337
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