Research workbench
Structure of the human CNOT1 superfamily homology domain in complex with a NANOS1 peptide
Analyse Structure of the human CNOT1 superfamily homology domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CQO
- Type
- protein
- Length
- 1,055 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 1; Nanos homolog 1
- UniProt
- A5YKK6, Q8WY41
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-not transcription complex subunit 1 | protein | 510 | 70% helix, 0% strand | A5YKK6 |
| B | Nanos homolog 1 | protein | 15 | 33% helix, 0% strand | Q8WY41 |
| C | CCR4-not transcription complex subunit 1 | protein | 516 | 71% helix, 0% strand | A5YKK6 |
| D | Nanos homolog 1 | protein | 14 | 36% helix, 0% strand | Q8WY41 |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.83 | 0.88 | 62 | empty |
| 2 | 492 | 0.72 | 0.81 | 61 | empty |
| 3 | 51 | 0.68 | 0.97 | 14 | empty |
| 4 | 526 | 0.67 | 0.77 | 70 | empty |
| 5 | 432 | 0.61 | 0.76 | 63 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1283 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 543 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 510 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 485 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4CQO · Structure of the human CNOT1 superfamily homology domain in complex with a Nanos1 peptide · the same entry in another collection · chain C against C, TM-score 1.00
- A5YKK6 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 1 (A5YKK6) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q8WY41 · AlphaFold monomer V2.0 prediction for nanos homolog 1 (Q8WY41) · a predicted model of the same protein · chain D against A, TM-score 0.40
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 A5YKK6
- Every structure of UniProt Q8WY41
- Elsewhere: RCSB PDB 4CQO · PDBe 4CQO · UniProt A5YKK6 · UniProt Q8WY41
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