MolNFT v2 · #222728 · protein
CCP5 in complex with Glu-P-peptide 2 transition state analog
8V3P · Cytosolic carboxypeptidase-like protein 5: “CCP5 in complex with Glu-P-peptide 2 transition state analog”. X-ray diffraction at 2.36, 1 ligand (ZN), 2 pockets (best druggability 0.48). MolNFT v2 #222728 on GenesisL1: 3D structure…
- PDB
- 8V3P
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.36
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Cytosolic carboxypeptidase-like protein 5; Tubulin beta-2A chain
- EC
- 3.4.17.-, 3.4.17.24
- UniProt
- Q8NDL9, Q13885
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · resolution 2.36 · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic carboxypeptidase-like protein 5 (EC 3.4.17.-, 3.4.17.24) | protein | 462 | 30% helix, 27% strand | Q8NDL9 |
| I | Tubulin beta-2A chain | protein | 1 | 0% helix, 0% strand | Q13885 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.48 | 0.85 | 18 | empty |
| 2 | 52 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–I · 332 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- Q8NDL9 · AlphaFold monomer V2.0 prediction for cytosolic carboxypeptidase-like protein 5 (Q8NDL9) · 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 Q8NDL9
- Every structure of UniProt Q13885
- Elsewhere: RCSB PDB 8V3P · PDBe 8V3P · UniProt Q8NDL9 · UniProt Q13885
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