MolNFT v1 · #164619 · protein
Thrombin in complex with a D-phe-pro-P-phenol derivative
6T3M · Prothrombin: “Thrombin in complex with a D-phe-pro-P-phenol derivative”. X-ray diffraction, 4 ligands (MD8, NAG, NA), 2 pockets (best druggability 0.55). MolNFT v1 #164619 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6T3M
- Type
- protein
- Length
- 291 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- MD8, NAG, NA, PO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 30 | 33% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 251 | 15% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 10 | 30% helix, 0% strand | P09945 |
Ligands and binding sites
- MD8 · (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)methyl]pyrrolidine-2-carboxamide · ligand · 2 copies · chains H, L
- 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
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 | 264 | 0.55 | 0.77 | 40 | MD8 |
| 2 | 201 | 0.49 | 0.75 | 23 | MD8 |
Interfaces
2 interfaces between chains.
- L–H · 1168 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 598 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 6T3M · Thrombin in Complex with a D-Phe-Pro-p-phenol derivative · the same entry in another collection · chain H against H, 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 P00734
- Every structure of UniProt P09945
- Elsewhere: RCSB PDB 6T3M · PDBe 6T3M · UniProt P00734 · UniProt P09945
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