Research workbench
Interaction of factor xiii activation peptide with alpha-thrombin: crystal structure of the enzyme-substrate complex
Analyse Interaction of factor xiii activation peptide with alpha-thrombin: crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DE7
- Type
- protein
- Length
- 574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (light chain); Alpha-thrombin (heavy chain); Factor xiii activation…
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NA, 0QE
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (light chain) (EC 3.4.21.5) | protein | 28 | 32% helix, 0% strand | P00734 |
| H | Alpha-thrombin (heavy chain) (EC 3.4.21.5) | protein | 249 | 14% helix, 35% strand | P00734 |
| J | Alpha-thrombin (light chain) (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| K | Alpha-thrombin (heavy chain) (EC 3.4.21.5) | protein | 251 | 12% helix, 35% strand | P00734 |
| A, B | Factor xiii activation peptide (28-37) | protein | 10 | 40% helix, 20% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains H, K
- 0QE · Chloromethane · ion · 2 copies · chains H, A, K, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.73 | 0.78 | 66 | empty |
| 2 | 65 | 0.37 | 0.78 | 19 | empty |
| 3 | 82 | 0.31 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1187 Ų buried · 26 hydrogen bonds · protein-protein
- J–K · 1104 Ų buried · 23 hydrogen bonds · protein-protein
- K–B · 687 Ų buried · 22 hydrogen bonds · protein-protein
- H–A · 650 Ų buried · 15 hydrogen bonds · protein-protein
- H–J · 219 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 1DE7 · Interaction of factor xiii activation peptide with alpha-thrombin: crystal structure of… · the same entry in another collection · chain L against L, 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 1DE7 · PDBe 1DE7 · UniProt P00734
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