MolNFT v2 · #113730 · protein
Thrombin in complex with 3-chloro-benzamide
5AFY · Prothrombin: “Thrombin in complex with 3-chloro-benzamide”. X-ray diffraction at 1.12, 4 ligands (WCE, NAG, NA), 2 pockets (best druggability 0.55). MolNFT v2 #113730 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AFY
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.12
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Prothrombin; Hirudin-2
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- WCE, NAG, NA, PO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · resolution 1.12 · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Prothrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| I | Hirudin-2 | protein | 12 | 25% helix, 0% strand | P28504 |
| L | Prothrombin (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
- WCE · 3-chloro-benzamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- PO4 · Phosphate ion · ion · chains H
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains H
- GOL · Glycerol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.55 | 0.77 | 37 | WCE |
| 2 | 56 | 0.28 | 0.74 | 13 | GOL |
Interfaces
2 interfaces between chains.
- H–L · 1123 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 630 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
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 P00734
- Every structure of UniProt P28504
- Elsewhere: RCSB PDB 5AFY · PDBe 5AFY · UniProt P00734 · UniProt P28504
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