MolNFT v1 · #184627 · protein
Structure of cyld cap-GLY3 (467-565) bound to ub; orthorhobic space group
7OWC · Ubiquitin-60S ribosomal protein L40: “Structure of cyld cap-GLY3 (467-565) bound to ub; orthorhobic space group”. X-ray diffraction, 2 pockets (best druggability 0.71). MolNFT v1 #184627 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7OWC
- Type
- protein
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-60S ribosomal protein L40; Deubiquitinating enzyme cyld
- UniProt
- P62987, J3KRR7
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-60S ribosomal protein L40 | protein | 74 | 24% helix, 35% strand | P62987 |
| B | Deubiquitinating enzyme cyld | protein | 95 | 17% helix, 37% strand | J3KRR7 |
| C | Ubiquitin-60S ribosomal protein L40 | protein | 73 | 25% helix, 36% strand | P62987 |
| D | Deubiquitinating enzyme cyld | protein | 94 | 7% helix, 37% strand | J3KRR7 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.71 | 0.76 | 93 | empty |
| 2 | 74 | 0.32 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 702 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 677 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 493 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7OWC · Structure of CYLD CAP-Gly3 (467-565) bound to Ub; orthorhobic space group · the same entry in another collection · chain A against A, TM-score 1.00
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P62987
- Every structure of UniProt J3KRR7
- Elsewhere: RCSB PDB 7OWC · PDBe 7OWC · UniProt P62987 · UniProt J3KRR7
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