Research workbench
1.9 ångström crystal structure of wild-type human thrombin in the sodium free state
Analyse 1.9 ångström crystal structure of wild-type human thrombin in the sodium free… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AFQ
- Type
- protein
- Length
- 541 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Prothrombin (EC 3.4.21.5) | protein | 29 | 31% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 245 | 16% helix, 36% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 238 | 16% helix, 37% strand | P00734 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.83 | 0.85 | 90 | GOL |
| 2 | 50 | 0.64 | 0.95 | 16 | empty |
| 3 | 55 | 0.49 | 0.86 | 19 | empty |
| 4 | 116 | 0.36 | 0.73 | 23 | empty |
| 5 | 65 | 0.36 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1194 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1156 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 943 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2AFQ · 1.9 angstrom crystal structure of wild-type human thrombin in the sodium free state · the same entry in another collection · chain A against A, 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 2AFQ · PDBe 2AFQ · UniProt P00734
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