MolNFT v1 · #86495 · protein
Nuclease module of the yeast CCR4-not complex
4B8C · POLY(A) ribonuclease POP2: “Nuclease module of the yeast CCR4-not complex”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #86495 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4B8C
- Type
- protein
- Length
- 3,056 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) ribonuclease POP2; General negative regulator of transcription subunit 1…
- EC
- 3.1.13.4
- UniProt
- P39008, P25655, P31384
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | POLY(A) ribonuclease POP2 (EC 3.1.13.4) | protein | 267 | 47% helix, 14% strand | P39008 |
| B, G, H, I | General negative regulator of transcription subunit 1 | protein | 233 | 64% helix, 2% strand | P25655 |
| D, K | Glucose-repressible alcohol dehydrogenase transcriptional effector (EC 3.1.13.4) | protein | 318 | 35% helix, 8% strand | P31384 |
| J, L | Glucose-repressible alcohol dehydrogenase transcriptional effector (EC 3.1.13.4) | protein | 210 | 38% helix, 5% strand | P31384 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.82 | 0.83 | 94 | empty |
| 2 | 1199 | 0.80 | 0.81 | 100 | empty |
| 3 | 258 | 0.72 | 0.87 | 43 | empty |
| 4 | 70 | 0.70 | 0.95 | 20 | empty |
| 5 | 68 | 0.69 | 0.95 | 19 | empty |
Interfaces
11 interfaces between chains.
- A–D · 1158 Ų buried · 15 hydrogen bonds · protein-protein
- C–K · 1150 Ų buried · 13 hydrogen bonds · protein-protein
- E–L · 1073 Ų buried · 12 hydrogen bonds · protein-protein
- C–H · 909 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4B8C · nuclease module of the yeast Ccr4-Not complex · 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 P39008
- Every structure of UniProt P25655
- Every structure of UniProt P31384
- Elsewhere: RCSB PDB 4B8C · PDBe 4B8C · UniProt P39008 · UniProt P25655 · UniProt P31384
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