Research workbench
Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N- (2-(aminomethyl)-5-chlorobenzyl) pyrrolidine-2-carboxamide
Analyse Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LPD
- Type
- protein
- Length
- 293 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 71U, NAG, NA, PO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 31 | 32% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 15% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
Ligands and binding sites
- 71U · (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]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
- GOL · Glycerol · additive · chains H
- DMS · Dimethyl sulfoxide · additive · 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 | 227 | 0.56 | 0.78 | 35 | GOL, 71U |
| 2 | 51 | 0.26 | 0.73 | 12 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1165 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 621 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 5LPD · Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(2-(aminomethyl)-5-ch… · 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 5LPD · PDBe 5LPD · UniProt P00734 · UniProt P09945
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