Research workbench
Thrombin in complex with 4-methoxy-N-(2-PYRIDINYL)BENZAMIDE
Analyse Thrombin in complex with 4-methoxy-N-(2-PYRIDINYL)BENZAMIDE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AF9
- Type
- protein
- Length
- 289 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, P09945
- Ligands
- SJR, NAG, NA, PO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% 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 | 11 | 27% helix, 0% strand | P09945 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
- SJR · 4-methoxy-N-(pyridin-2-yl)benzamide · 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 · 3 copies · chains H
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains H
- EDO · 1,2-ethanediol · 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 | 283 | 0.56 | 0.76 | 39 | SJR |
| 2 | 50 | 0.26 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1108 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 613 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 5AF9 · Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide · 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 5AF9 · PDBe 5AF9 · UniProt P00734 · UniProt P09945
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