MolNFT v1 · #105953 · protein
Crystal structure of thrombin mutant S195T bound with ppack
4RKO · Thrombin heavy chain: “Crystal structure of thrombin mutant S195T bound with ppack”. X-ray diffraction, 3 ligands (0G6, NAG, NA), 2 pockets (best druggability 0.57). MolNFT v1 #105953 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RKO
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy chain; Thrombin light chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, NA
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| A | Thrombin light chain (EC 3.4.21.5) | protein | 40 | 40% helix, 0% strand | P00734 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 2 copies · chains B, A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.57 | 0.78 | 37 | 0G6 |
| 2 | 51 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1608 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, 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
- Elsewhere: RCSB PDB 4RKO · PDBe 4RKO · UniProt P00734
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