MolNFT v1 · #127276 · protein
Crystal structure of human carboxypeptidase O in complex with nvci
5MRV: “Crystal structure of human carboxypeptidase O in complex with nvci”. X-ray diffraction, 2 ligands (NAG, ZN), 3 pockets (best druggability 0.54). MolNFT v1 #127276 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MRV
- Type
- protein
- Length
- 667 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase O; Metallocarboxypeptidase inhibitor
- EC
- 3.4.17.-
- UniProt
- Q8IVL8, P86912
- Ligands
- NAG, ZN
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxypeptidase O (EC 3.4.17.-) | protein | 307 | 39% helix, 19% strand | Q8IVL8 |
| C | Metallocarboxypeptidase inhibitor | protein | 53 | 0% helix, 40% strand | P86912 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, B
- ZN · Zinc ion · metal · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.54 | 0.81 | 24 | empty |
| 2 | 308 | 0.54 | 0.75 | 26 | empty |
| 3 | 102 | 0.53 | 0.83 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–C · 933 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 743 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5MRV · Crystal structure of human carboxypeptidase O in complex with NvCI · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IVL8 · AlphaFold monomer V2.0 prediction for carboxypeptidase O (Q8IVL8) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P86912 · AlphaFold monomer V2.0 prediction for metallocarboxypeptidase inhibitor (P86912) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 Q8IVL8
- Every structure of UniProt P86912
- Elsewhere: RCSB PDB 5MRV · PDBe 5MRV · UniProt Q8IVL8 · UniProt P86912
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