MolNFT v1 · #64944 · protein
Structure of thrombin mutant DELTA(146-149E) in the free form
3GIC · Thrombin light chain: “Structure of thrombin mutant DELTA(146-149E) in the free form”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.54). MolNFT v1 #64944 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3GIC
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- 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
- NAG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 248 | 14% helix, 33% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.54 | 0.80 | 25 | empty |
| 2 | 89 | 0.43 | 0.79 | 27 | empty |
| 3 | 58 | 0.31 | 0.76 | 17 | empty |
| 4 | 57 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1188 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3GIC · Structure of thrombin mutant delta(146-149e) in the free form · 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 3GIC · PDBe 3GIC · UniProt P00734
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