Research workbench
Crystal structure of prothrombin deletion mutant residues 154-167 ( form I )
Analyse Crystal structure of prothrombin deletion mutant residues 154-167 ( form I ) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EDM
- Type
- protein
- Length
- 550 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, SO4
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 550 | 22% helix, 20% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MG · Magnesium ion · metal · 6 copies · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.59 | 0.78 | 44 | GOL |
| 2 | 138 | 0.53 | 0.81 | 22 | empty |
| 3 | 110 | 0.49 | 0.81 | 24 | empty |
| 4 | 62 | 0.47 | 0.84 | 23 | empty |
| 5 | 164 | 0.45 | 0.75 | 26 | empty |
Modifications
Observed in the structure: 12 disulfide, 10 modified, 3 glycan (disulfide, carboxylation, N-glycosylation).
Compared structures
- 5EDM · Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I ) · 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 5EDM · PDBe 5EDM · UniProt P00734
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