Research workbench
2.2 ångström crystal structure of the complex between bovine thrombin and sucrose octasulfate
Analyse 2.2 ångström crystal structure of the complex between bovine thrombin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PMA
- Type
- protein
- Length
- 555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00735
- Ligands
- GU4, YYJ, NA
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 38% helix, 0% strand | P00735 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 238 | 13% helix, 36% strand | P00735 |
| D | Thrombin heavy chain (EC 3.4.21.5) | protein | 259 | 14% helix, 33% strand | P00735 |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · 2 copies · chains D, B
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains B, D
- CIT · Citric acid · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.63 | 0.77 | 45 | empty |
| 2 | 229 | 0.52 | 0.76 | 29 | empty |
| 3 | 208 | 0.50 | 0.76 | 34 | empty |
| 4 | 73 | 0.48 | 0.83 | 18 | empty |
| 5 | 72 | 0.38 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1238 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1173 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 449 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3PMA · 2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose… · the same entry in another collection · chain B against B, 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 P00735
- Elsewhere: RCSB PDB 3PMA · PDBe 3PMA · UniProt P00735
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