MolNFT v1 · #9985 · protein
Crystal structure of bovine thrombin complex with protease inhibitor ecotin
1ID5: “Crystal structure of bovine thrombin complex with protease inhibitor ecotin”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.57). MolNFT v1 #9985 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ID5
- Type
- protein
- Length
- 424 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Ecotin
- EC
- 3.4.21.5
- UniProt
- P00735, P23827
- Ligands
- CA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin (EC 3.4.21.5) | protein | 30 | 37% helix, 0% strand | P00735 |
| H | Thrombin (EC 3.4.21.5) | protein | 256 | 12% helix, 32% strand | P00735 |
| I | Ecotin | protein | 138 | 7% helix, 49% strand | P23827 |
Ligands and binding sites
- CA · Calcium ion · metal · chains H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.57 | 0.83 | 22 | empty |
| 2 | 250 | 0.53 | 0.76 | 35 | empty |
| 3 | 54 | 0.38 | 0.80 | 19 | empty |
| 4 | 75 | 0.38 | 0.77 | 15 | TRS |
| 5 | 56 | 0.36 | 0.79 | 12 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1182 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 1179 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1ID5 · Crystal structure of bovine thrombin complex with protease inhibitor ecotin · the same entry in another collection · chain L against L, TM-score 1.00
- P23827 · AlphaFold monomer V2.0 prediction for ecotin (P23827) · a predicted model of the same protein · chain I against A, TM-score 0.97
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain H against A, TM-score 0.96
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 P00735
- Every structure of UniProt P23827
- Elsewhere: RCSB PDB 1ID5 · PDBe 1ID5 · UniProt P00735 · UniProt P23827
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