Research workbench
Staphylocoagulase bound to bovine thrombin
Analyse Staphylocoagulase bound to bovine thrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A1D
- Type
- protein
- Length
- 1,164 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Staphylocoagulase
- EC
- 3.4.21.5
- UniProt
- P00735, P17855
- Ligands
- 0G6, NAG, NA
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Thrombin (EC 3.4.21.5) | protein | 41 | 34% helix, 0% strand | P00735 |
| B, F | Thrombin (EC 3.4.21.5) | protein | 259 | 11% helix, 33% strand | P00735 |
| D, H | Staphylocoagulase | protein | 282 | 62% helix, 0% strand | P17855 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains B, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.79 | 0.81 | 117 | 0G6 |
| 2 | 1198 | 0.76 | 0.78 | 125 | 0G6 |
| 3 | 310 | 0.60 | 0.78 | 41 | empty |
| 4 | 355 | 0.59 | 0.76 | 35 | empty |
| 5 | 357 | 0.58 | 0.76 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1856 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 1842 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1563 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1560 Ų buried · 29 hydrogen bonds · protein-protein
- D–H · 647 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 2A1D · Staphylocoagulase bound to bovine thrombin · the same entry in another collection · chain E against E, TM-score 1.00
- P17855 · AlphaFold monomer V2.0 prediction for staphylocoagulase (P17855) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain F against A, TM-score 0.96
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
- Every structure of UniProt P17855
- Elsewhere: RCSB PDB 2A1D · PDBe 2A1D · UniProt P00735 · UniProt P17855
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