Research workbench
Slow form of thrombin bound with ppack
Analyse Slow form of thrombin bound with ppack in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SHH
- Type
- protein
- Length
- 567 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin | protein | 29 | 34% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 252 | 14% helix, 35% strand | P00734 |
| D | Thrombin | protein | 29 | 41% helix, 0% strand | P00734 |
| E | Thrombin (EC 3.4.21.5) | protein | 257 | 15% helix, 34% 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 · 2 copies · chains B, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.62 | 0.78 | 42 | 0G6 |
| 2 | 205 | 0.55 | 0.79 | 35 | 0G6 |
| 3 | 71 | 0.34 | 0.76 | 20 | empty |
| 4 | 98 | 0.33 | 0.72 | 24 | empty |
| 5 | 78 | 0.31 | 0.73 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1188 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1095 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 622 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 199 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
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 1SHH · PDBe 1SHH · UniProt P00734
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