MolNFT v1 · #119889 · protein
Crystal structure of thrombin-avathrin complex
5GIM · Thrombin light chain: “Crystal structure of thrombin-avathrin complex”. X-ray diffraction, 2 pockets (best druggability 0.53). MolNFT v1 #119889 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GIM
- Type
- protein
- Length
- 298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; N-terminal peptide from putative…
- EC
- 3.4.21.5
- UniProt
- P00734, Q6F3E8
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 33% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 15% helix, 34% strand | P00734 |
| C | N-terminal peptide from putative uncharacterized protein avahiru | protein | 6 | 0% helix, 17% strand | Q6F3E8 |
| D | C-terminal peptide from putative uncharacterized protein avahiru | protein | 10 | 30% helix, 0% strand | Q6F3E8 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.53 | 0.78 | 31 | empty |
| 2 | 130 | 0.43 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1155 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 544 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GIM · Crystal structure of thrombin-avathrin complex · 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
- Every structure of UniProt Q6F3E8
- Elsewhere: RCSB PDB 5GIM · PDBe 5GIM · UniProt P00734 · UniProt Q6F3E8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.