Research workbench
Crystal structure of human thrombin mutant I16T
Analyse Crystal structure of human thrombin mutant I16T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PXJ
- Type
- protein
- Length
- 552 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
- P00734
- Ligands
- MG
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 34 | 35% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 245 | 17% helix, 36% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 245 | 17% helix, 38% strand | P00734 |
| A | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
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 | 1027 | 0.82 | 0.84 | 95 | GOL, MG |
| 2 | 156 | 0.42 | 0.74 | 23 | empty |
| 3 | 79 | 0.35 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1403 Ų buried · 27 hydrogen bonds · protein-protein
- B–A · 1154 Ų buried · 26 hydrogen bonds · protein-protein
- H–B · 992 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6PXJ · Crystal structure of human thrombin mutant I16T · 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 6PXJ · PDBe 6PXJ · UniProt P00734
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