MolNFT v1 · #117617 · protein
Crystal structure of prothrombin deletion mutant residues 146-167 ( form II ).
5EDK: “Crystal structure of prothrombin deletion mutant residues 146-167 ( form II ).”. X-ray diffraction, 2 ligands (NAG, MG), 9 pockets (best druggability 0.62). MolNFT v1 #117617 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5EDK
- Type
- protein
- Length
- 528 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, MG
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 528 | 14% helix, 19% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.62 | 0.86 | 20 | empty |
| 2 | 207 | 0.55 | 0.79 | 38 | empty |
| 3 | 246 | 0.52 | 0.76 | 25 | empty |
| 4 | 227 | 0.50 | 0.75 | 28 | empty |
| 5 | 77 | 0.41 | 0.79 | 21 | empty |
Modifications
Observed in the structure: 12 disulfide, 10 modified, 3 glycan (disulfide, carboxylation, N-glycosylation).
Compared structures
- 5EDK · Crystal structure of prothrombin deletion mutant residues 146-167 ( Form II ). · 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 5EDK · PDBe 5EDK · UniProt P00734
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