MolNFT v1 · #123933 · protein
Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N- (4-CARBAMIMIDOYLBENZYL)PYRROLIDINE-2-carboxamide
5JZY · Prothrombin: “Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N…”. X-ray diffraction, 4 ligands (6OV, NAG, NA), 2 pockets (best druggability 0.52). MolNFT v1 #123933 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JZY
- 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
- 6OV, NAG, NA, PO4
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 29 | 45% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 12 | 25% helix, 0% strand | P09945 |
Ligands and binding sites
- 6OV · 3-cyclohexyl-D-alanyl-N-[(4-carbamimidoylphenyl)methyl]-L-prolinamide · 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 · 3 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 | 199 | 0.52 | 0.77 | 39 | 6OV |
| 2 | 72 | 0.33 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1137 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 623 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 5JZY · Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzy… · the same entry in another collection · chain L against L, 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 5JZY · PDBe 5JZY · UniProt P00734 · UniProt P09945
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