Research workbench
Carboxypeptidase a complexed with 2-benzyl-3-iodo-propanoic acid (bip)
Analyse Carboxypeptidase a complexed with 2-benzyl-3-iodo-propanoic acid (bip) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BAV
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase a
- EC
- 3.4.17.1
- UniProt
- P00730
- Ligands
- BIP, ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Carboxypeptidase a (EC 3.4.17.1) | protein | 307 | 38% helix, 16% strand | P00730 |
Ligands and binding sites
- BIP · 2-benzyl-3-iodopropanoic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.80 | 0.82 | 83 | BIP |
| 2 | 1064 | 0.79 | 0.80 | 98 | BIP |
| 3 | 620 | 0.65 | 0.75 | 49 | empty |
| 4 | 95 | 0.59 | 0.87 | 26 | BIP |
| 5 | 95 | 0.58 | 0.87 | 26 | BIP |
Interfaces
5 interfaces between chains.
- A–B · 446 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 445 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 147 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 134 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 1BAV · Carboxypeptidase a complexed with 2-benzyl-3-iodo-propanoic acid (bip) · 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 A 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 1BAV · PDBe 1BAV · UniProt P00730
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