Research workbench
SER195ALA mutant of human thrombin complexed with fibrinopeptide a (7- 16)
Analyse SER195ALA mutant of human thrombin complexed with fibrinopeptide a (7- 16) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DM4
- Type
- protein
- Length
- 295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (alpha THROMBIN:LIGHT chain); Protein (mutant alpha THROMBIN:HEAVY chain)…
- UniProt
- P00734
- Ligands
- ACE
- Pockets
- 3 · best druggability 0.33
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (alpha THROMBIN:LIGHT chain) | protein | 33 | 30% helix, 3% strand | P00734 |
| B | Protein (mutant alpha THROMBIN:HEAVY chain) | protein | 252 | 14% helix, 34% strand | P00734 |
| C | Protein (fibrinopeptide) | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.33 | 0.76 | 17 | empty |
| 2 | 50 | 0.32 | 0.78 | 16 | empty |
| 3 | 67 | 0.32 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1431 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 681 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1DM4 · SER195ALA mutant of human thrombin complexed with fibrinopeptide a (7-16) · 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 1DM4 · PDBe 1DM4 · UniProt P00734
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