Research workbench
Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl- N-((1-carbamimidoyl-4-PIPERIDINYL)METHYL)-L-prolinamide (bms-189664)
Analyse Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TU7
- Type
- protein
- Length
- 292 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
- 0BM
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% 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 | 250 | 15% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
Ligands and binding sites
- 0BM · N-(methylsulfonyl)-D-phenylalanyl-N-[(1-carbamimidoylpiperidin-4-yl)methyl]-L-prolinamide · ligand · 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 | 231 | 0.58 | 0.79 | 40 | 0BM |
| 2 | 57 | 0.49 | 0.86 | 17 | empty |
| 3 | 58 | 0.34 | 0.77 | 19 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1297 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 657 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 3TU7 · Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl-N-((1-carbamimidoyl… · 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 3TU7 · PDBe 3TU7 · UniProt P00734 · UniProt P09945
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