MolNFT v1 · #78388 · protein
Structure of thrombin mutant Y225P in the E form
3S7K · Prothrombin: “Structure of thrombin mutant Y225P in the E form”. X-ray diffraction, 1 ligand (K), 8 pockets (best druggability 0.60). MolNFT v1 #78388 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3S7K
- Type
- protein
- Length
- 567 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- K
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 31 | 39% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 252 | 14% helix, 34% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 33 | 45% helix, 0% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 251 | 14% helix, 34% strand | P00734 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.60 | 0.78 | 43 | empty |
| 2 | 225 | 0.52 | 0.76 | 35 | empty |
| 3 | 98 | 0.51 | 0.83 | 27 | empty |
| 4 | 123 | 0.48 | 0.79 | 29 | empty |
| 5 | 79 | 0.40 | 0.78 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1236 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 160 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3S7K · Structure of thrombin mutant Y225P in the E form · the same entry in another collection · chain C against C, 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 3S7K · PDBe 3S7K · UniProt P00734
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