Research workbench
Human alpha-thrombin complexed with [S-(R*,R*)]-4-[(aminoiminomethyl) amino]-N-[[1-[3-hydroxy-2-[(2-NAPHTHALENYLSULFONYL)AMINO]-1- oxopropyl]-2-pyrrolidinyl] METHYL]BUTANAMIDE (bms-186282)
Analyse Human alpha-thrombin complexed with [S-(R*,R*)]-4-[(aminoiminomethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BMM
- Type
- protein
- Length
- 295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirudin I
- EC
- 3.4.21.5
- UniProt
- P00734, P28507
- Ligands
- BM2
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 258 | 14% helix, 33% strand | P00734 |
| I | Hirudin I | protein | 9 | 0% helix, 0% strand | P28507 |
Ligands and binding sites
- BM2 · S-(R*,R*)]-4-[aminoiminomethyl)amino]-N-[[1-[3-hydroxy -2-[(2-naphthalenylsulfonyl)amino]-1-oxopropyl]-2-pyrrolidinyl] methyl]butanamide · ligand · 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 | 286 | 0.57 | 0.77 | 43 | BM2 |
| 2 | 101 | 0.38 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1179 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 567 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1BMM · Human alpha-thrombin complexed with [S-(R*,R*)]-4-[(AMINOIMINOMETHYL)AMINO]-N-[[1-[3-hydro… · the same entry in another collection · chain L against L, TM-score 1.00
- P28507 · AlphaFold monomer V2.0 prediction for hirudin-3A (P28507) · a predicted model of the same protein · chain I against A, TM-score 0.58
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 P28507
- Elsewhere: RCSB PDB 1BMM · PDBe 1BMM · UniProt P00734 · UniProt P28507
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