Research workbench
Bovine prothrombin fragment 1 in complex with calcium and lysophosphotidylserine
Analyse Bovine prothrombin fragment 1 in complex with calcium and lysophosphotidylserine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NL2
- Type
- protein
- Length
- 146 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00735
- Ligands
- LPS, NAG, CA, CL
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 146 | 27% helix, 10% strand | P00735 |
Ligands and binding sites
- LPS · O-{hydroxy[((2r)-2-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propyl)oxy]phosphoryl}-L-serine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 7 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Modifications
Observed in the structure: 10 modified, 5 disulfide, 2 glycan (carboxylation, disulfide, N-glycosylation).
Compared structures
- 1NL2 · Bovine prothrombin fragment 1 in complex with calcium and lysophosphotidylserine · the same entry in another collection · chain A against A, TM-score 1.00
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00735
- Elsewhere: RCSB PDB 1NL2 · PDBe 1NL2 · UniProt P00735
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