Research workbench
Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-oxo-propyl)-3-phenyl-propanamide
Analyse Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AFZ
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy chain; Hirudin variant-2; Thrombin light chain
- EC
- 3.4.21.5
- UniProt
- P00734, P28511
- Ligands
- UET, TYS, NAG, NA, PO4
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 8 | 0% helix, 0% strand | P28511 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
- UET · N-(benzylsulfonyl)-D-phenylalanyl-N-(4-carbamimidoylbenzyl)glycinamide · ligand · chains H
- TYS · O-sulfo-L-tyrosine · ligand · chains H, I
- 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.51 | 0.77 | 38 | UET |
| 2 | 65 | 0.34 | 0.77 | 17 | TYS |
| 3 | 50 | 0.29 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1118 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 453 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 5AFZ · Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4… · the same entry in another collection · chain H against H, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.93
- P28511 · AlphaFold monomer V2.0 prediction for hirudin-3B' (P28511) · a predicted model of the same protein · chain I against A, TM-score 0.62
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 P28511
- Elsewhere: RCSB PDB 5AFZ · PDBe 5AFZ · UniProt P00734 · UniProt P28511
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.