Research workbench
Crystal structure of Thrombin bound to P2 macrocycle
Analyse Crystal structure of Thrombin bound to P2 macrocycle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GWE
- Type
- protein
- Length
- 559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- Thrombin heavy chain; Thrombin light chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- ODB, NAG, NA
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 15% helix, 36% strand | P00734 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 30% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 35% strand | P00734 |
| B | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 43% helix, 0% strand | P00734 |
Ligands and binding sites
- ODB · (10S,14S,17R)-14-(3-carbamimidamidopropyl)-3-[[2-(hydroxymethyl)phenyl]methyl]-5,12,15-tris(oxidanylidene)-19-thia-3,6,13,16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(21),22,24-triene-17-carboxamide · ligand · 2 copies · chains A, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H
- NA · Sodium ion · metal · 2 copies · chains A, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.59 | 0.78 | 39 | ODB |
| 2 | 325 | 0.57 | 0.76 | 41 | empty |
| 3 | 216 | 0.55 | 0.78 | 39 | ODB |
| 4 | 111 | 0.42 | 0.76 | 28 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 1187 Ų buried · 28 hydrogen bonds · protein-protein
- L–H · 1173 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 378 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 162 Ų buried · 2 hydrogen bonds · protein-protein
- H–B · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6GWE · Crystal structure of thrombin bound to P2 macrocycle · the same entry in another collection · chain A against A, 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 6GWE · PDBe 6GWE · UniProt P00734
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