MolNFT v1 · #86518 · protein
Pvhl-elob-elob-eloc COMPLEX_(2S,4R)-1-(2-CHLOROPHENYL)CARBONYL-N-[(4- CHLOROPHENYL)METHYL]-4-oxidanyl-pyrrolidine-2-carboxamide bound
4B95 · Transcription elongation factor B polypeptide 2: “Pvhl-elob-elob-eloc COMPLEX_(2S,4R)-1-(2-CHLOROPHENYL)CARBONYL-N-[(4…”. X-ray diffraction, 1 ligand (UCK), 10 pockets (best druggability 0.57). MolNFT v1 #86518 on GenesisL1: 3D…
- PDB
- 4B95
- Type
- protein
- Length
- 1,308 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
- UCK
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 11 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription elongation factor B polypeptide 2 | protein | 104 | 17% helix, 37% strand | Q15370 |
| B, E | Transcription elongation factor B polypeptide 1 | protein | 87 | 47% helix, 15% strand | Q15369 |
| C | Von hippel-lindau disease tumor suppressor | protein | 134 | 25% helix, 31% strand | P40337 |
| D | Transcription elongation factor B polypeptide 2 | protein | 95 | 16% helix, 34% strand | Q15370 |
| F | Von hippel-lindau disease tumor suppressor | protein | 139 | 25% helix, 30% strand | P40337 |
| G | Transcription elongation factor B polypeptide 2 | protein | 103 | 15% helix, 37% strand | Q15370 |
| H | Transcription elongation factor B polypeptide 1 | protein | 87 | 47% helix, 15% strand | Q15369 |
| I | Von hippel-lindau disease tumor suppressor | protein | 144 | 26% helix, 29% strand | P40337 |
| J | Transcription elongation factor B polypeptide 2 | protein | 102 | 15% helix, 37% strand | Q15370 |
| K | Transcription elongation factor B polypeptide 1 | protein | 86 | 48% helix, 15% strand | Q15369 |
| L | Von hippel-lindau disease tumor suppressor | protein | 140 | 23% helix, 29% strand | P40337 |
Ligands and binding sites
- UCK · (2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 4 copies · chains C, F, I, L
- ACT · Acetate ion · additive · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.57 | 0.77 | 34 | UCK |
| 2 | 283 | 0.57 | 0.77 | 41 | UCK |
| 3 | 57 | 0.48 | 0.85 | 14 | empty |
| 4 | 94 | 0.45 | 0.80 | 29 | empty |
| 5 | 52 | 0.40 | 0.81 | 19 | empty |
Interfaces
16 interfaces between chains.
- J–K · 1157 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1123 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1090 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1076 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1067 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4B95 · pVHL-EloB-EloB-EloC complex_(2S,4R)-1-(2-chlorophenyl)carbonyl-N-[(4-chlorophenyl)methyl]… · 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 4B95 · PDBe 4B95 · UniProt Q15370 · UniProt Q15369 · UniProt P40337
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