Research workbench
Human thrombin complexed with D-phe-pro-D-arg-D-thr
Analyse Human thrombin complexed with D-phe-pro-D-arg-D-thr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U8O
- Type
- protein
- Length
- 285 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; D-phe-pro-D-arg-D-thr derived direct thrombin…
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, NA, NH2, IOD, CL
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 43% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | D-phe-pro-D-arg-D-thr derived direct thrombin inhibitor | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · chains H
- NH2 · Amino group · ion · chains H, I
- IOD · Iodide ion · ion · chains H
- CL · Chloride ion · ion · chains H
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.36 | 0.74 | 16 | empty |
| 2 | 68 | 0.34 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1225 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 518 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 d-amino, 1 glycan (disulfide, D-amino acid, N-glycosylation).
Compared structures
- 3U8O · Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr · 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 3U8O · PDBe 3U8O · UniProt P00734
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