Research workbench
Human thrombin chimera with human residues 184A, 186, 186A, 186B, 186C and 222 replaced by murine thrombin equivalents.
Analyse Human thrombin chimera with human residues 184A, 186, 186A, 186B, 186C and 222… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OD3
- Type
- protein
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- UniProt
- P00734
- Ligands
- 0G6, NAG
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain | protein | 28 | 36% helix, 0% strand | P00734 |
| B | Thrombin heavy chain | protein | 249 | 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 · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.54 | 0.79 | 30 | 0G6 |
Interfaces
1 interface between chains.
- A–B · 1142 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 2OD3 · Human thrombin chimera with human residues 184a, 186, 186a, 186b, 186c and 222 replaced… · the same entry in another collection · chain A against A, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 2OD3 · PDBe 2OD3 · UniProt P00734
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