Research workbench
Crystal structure of thrombin in complex with macrocycle N14-PR4-a
Analyse Crystal structure of thrombin in complex with macrocycle N14-PR4-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T7H
- Type
- protein
- Length
- 579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- MRQ, NAG, NA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 40% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 258 | 15% helix, 34% strand | P00734 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 34 | 35% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 13% helix, 34% strand | P00734 |
Ligands and binding sites
- MRQ · (14S,17R)-14-(3-carbamimidamidopropyl)-3-(furan-2-ylmethyl)-5,12,15-tris(oxidanylidene)-19-thia-3,6,13, 16-tetrazatricyclo[19.4.0.0^{6,10}]pentacosa-1(25),7, 9,21,23-pentaene-17-carboxamide · ligand · 2 copies · chains B, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, H
- NA · Sodium ion · metal · 2 copies · chains B, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.81 | 0.83 | 98 | EDO, MRQ |
| 2 | 317 | 0.61 | 0.79 | 52 | MRQ |
| 3 | 50 | 0.31 | 0.77 | 15 | empty |
| 4 | 63 | 0.30 | 0.74 | 11 | empty |
| 5 | 50 | 0.23 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1352 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 26 hydrogen bonds · protein-protein
- B–H · 672 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6T7H · Crystal structure of Thrombin in complex with macrocycle N14-PR4-A · 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 6T7H · PDBe 6T7H · UniProt P00734
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