Research workbench
THROMBIN:SURAMIN complex
Analyse THROMBIN:SURAMIN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BF6
- Type
- protein
- Length
- 281 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin, light chain; Thrombin, heavy chain; Phe-pro-arg
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- SVR
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin, light chain (EC 3.4.21.5) | protein | 28 | 29% helix, 0% strand | P00734 |
| H | Thrombin, heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 35% strand | P00734 |
| I | Phe-pro-arg | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.44 | 0.76 | 19 | empty |
| 2 | 55 | 0.28 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1216 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 448 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BF6 · Thrombin:suramin complex · 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
- Elsewhere: RCSB PDB 3BF6 · PDBe 3BF6 · UniProt P00734
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