MolNFT v1 · #2868 · protein
Complex of bdellastasin with porcine trypsin
1C9P: “Complex of bdellastasin with porcine trypsin”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.44). MolNFT v1 #2868 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1C9P
- Type
- protein
- Length
- 273 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin; Bdellastasin
- EC
- 3.4.21.4
- UniProt
- P00761, P82107
- Ligands
- CA
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypsin (EC 3.4.21.4) | protein | 223 | 10% helix, 38% strand | P00761 |
| B | Bdellastasin | protein | 50 | 0% helix, 36% strand | P82107 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.44 | 0.76 | 18 | empty |
| 2 | 61 | 0.34 | 0.77 | 17 | empty |
| 3 | 66 | 0.27 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1C9P · Complex of bdellastasin with porcine trypsin · the same entry in another collection · chain A against A, TM-score 1.00
- P00761 · AlphaFold monomer V2.0 prediction for trypsin (P00761) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P82107 · AlphaFold monomer V2.0 prediction for bdellastasin (P82107) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 P00761
- Every structure of UniProt P82107
- Elsewhere: RCSB PDB 1C9P · PDBe 1C9P · UniProt P00761 · UniProt P82107
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