Research workbench
Crystal structure for the complex of thrombin mutant D102N and hirudin
Analyse Crystal structure for the complex of thrombin mutant D102N and hirudin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MLF
- Type
- protein
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin variant-1
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- NAG, NA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 32 | 31% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 259 | 14% helix, 35% strand | P00734 |
| D | Hirudin variant-1 | protein | 61 | 0% helix, 31% strand | P01050 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · chains B
- ACT · Acetate ion · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.75 | 0.92 | 27 | empty |
| 2 | 275 | 0.53 | 0.75 | 26 | empty |
| 3 | 83 | 0.35 | 0.76 | 22 | empty |
| 4 | 52 | 0.27 | 0.74 | 16 | ACT |
Interfaces
2 interfaces between chains.
- B–D · 1637 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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
- Every structure of UniProt P01050
- Elsewhere: RCSB PDB 4MLF · PDBe 4MLF · UniProt P00734 · UniProt P01050
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