Research workbench
X-ray crystallographic studies on the complex of carboxypeptidase a with the inhibitor using alpha-nitro ketone as the zinc-binding group
Analyse X-ray crystallographic studies on the complex of carboxypeptidase a with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FX6
- Type
- protein
- Length
- 921 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase A1
- EC
- 3.4.17.1
- UniProt
- P00730
- Ligands
- BPX, ZN
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Carboxypeptidase A1 (EC 3.4.17.1) | protein | 307 | 38% helix, 17% strand | P00730 |
Ligands and binding sites
- BPX · (2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid · ligand · 3 copies · chains A, C, E
- ZN · Zinc ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.81 | 0.83 | 91 | BPX |
| 2 | 151 | 0.62 | 0.85 | 26 | BPX |
| 3 | 145 | 0.62 | 0.85 | 27 | BPX |
| 4 | 186 | 0.44 | 0.74 | 25 | empty |
| 5 | 119 | 0.42 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 576 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 193 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3FX6 · X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P00730 · AlphaFold monomer V2.0 prediction for carboxypeptidase A1 (P00730) · a predicted model of the same protein · chain E against A, 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 P00730
- Elsewhere: RCSB PDB 3FX6 · PDBe 3FX6 · UniProt P00730
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