MolNFT v1 · #160882 · protein
Crystal structure of human meizothrombin DESF1 mutant S195A bound with ppack
6PX5 · Prothrombin: “Crystal structure of human meizothrombin DESF1 mutant S195A bound with ppack”. X-ray diffraction, 4 ligands (0G6, NAG, ZN), 7 pockets (best druggability 0.69). MolNFT v1 #160882 on GenesisL1: 3D structure, binding…
- PDB
- 6PX5
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, ZN, NA
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Prothrombin (EC 3.4.21.5) | protein | 140 | 15% helix, 8% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 248 | 14% helix, 35% 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 · 2 copies · chains X, B
- ZN · Zinc ion · metal · 2 copies · chains X, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.69 | 0.81 | 43 | empty |
| 2 | 63 | 0.69 | 0.96 | 19 | empty |
| 3 | 221 | 0.60 | 0.81 | 37 | 0G6 |
| 4 | 157 | 0.46 | 0.76 | 21 | empty |
| 5 | 100 | 0.42 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- X–B · 3208 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 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 6PX5 · PDBe 6PX5 · UniProt P00734
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