MolNFT v1 · #164923 · protein
Thrombin in complex with a D-diphe-pro-P-pyridine derivative
6TDT · Prothrombin: “Thrombin in complex with a D-diphe-pro-P-pyridine derivative”. X-ray diffraction, 4 ligands (LXW, NAG, NA), 1 pocket (best druggability 0.52). MolNFT v1 #164923 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6TDT
- Type
- protein
- Length
- 293 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
- LXW, NAG, NA, PO4
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Prothrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| L | Prothrombin (EC 3.4.21.5) | protein | 31 | 32% helix, 0% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 36% helix, 0% strand | P09945 |
Ligands and binding sites
- LXW · (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide · 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 · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.52 | 0.77 | 38 | LXW |
Interfaces
2 interfaces between chains.
- H–L · 1188 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 605 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 6TDT · Thrombin in Complex with a D-DiPhe-Pro-p-pyridine 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 6TDT · PDBe 6TDT · UniProt P00734 · UniProt P09945
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