Research workbench
Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1- ((benzylsulfonyl)-D-ARGINYL)PYRROLIDINE-2-carboxamide
Analyse Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JFD
- Type
- protein
- Length
- 294 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
- 2TS, NAG, NA
- Pockets
- 2 · best druggability 0.57
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 | 31 | 32% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 252 | 15% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 36% helix, 0% strand | P09945 |
Ligands and binding sites
- 2TS · (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]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
- GOL · Glycerol · additive · 2 copies · 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 | 281 | 0.57 | 0.77 | 40 | 2TS, GOL |
| 2 | 56 | 0.29 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1177 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 608 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 5JFD · Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-argi… · 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 5JFD · PDBe 5JFD · UniProt P00734 · UniProt P09945
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