MolNFT v1 · #30609 · protein
Crystal structure of the complex between thrombin and the central "E" region of fibrin
2A45 · Thrombin light chain: “Crystal structure of the complex between thrombin and the central "E" region of fibrin”. X-ray diffraction, 2 ligands (0G6, PO4), 16 pockets (best druggability 0.77). MolNFT v1 #30609 on GenesisL1: 3D…
- PDB
- 2A45
- Type
- protein
- Length
- 864 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Fibrinogen alpha chain; Fibrinogen beta…
- EC
- 3.4.21.5
- UniProt
- P00734, P02671, P02675, P02679
- Ligands
- 0G6, PO4
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Thrombin light chain (EC 3.4.21.5) | protein | 32 | 19% helix, 0% strand | P00734 |
| B, E | Thrombin heavy chain (EC 3.4.21.5) | protein | 258 | 13% helix, 28% strand | P00734 |
| G, J | Fibrinogen alpha chain | protein | 48 | 52% helix, 4% strand | P02671 |
| H, K | Fibrinogen beta chain | protein | 52 | 50% helix, 12% strand | P02675 |
| I | Fibrinogen gamma chain | protein | 40 | 58% helix, 8% strand | P02679 |
| L | Fibrinogen gamma chain | protein | 44 | 59% helix, 2% strand | P02679 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains B, E
- PO4 · Phosphate ion · ion · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.77 | 0.79 | 114 | 0G6, PO4 |
| 2 | 79 | 0.63 | 0.90 | 23 | empty |
| 3 | 140 | 0.61 | 0.84 | 24 | empty |
| 4 | 128 | 0.60 | 0.84 | 20 | empty |
| 5 | 298 | 0.58 | 0.77 | 47 | 0G6, PO4 |
Interfaces
22 interfaces between chains.
- A–B · 1143 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1096 Ų buried · 26 hydrogen bonds · protein-protein
- H–J · 726 Ų buried · 9 hydrogen bonds · protein-protein
- I–L · 721 Ų buried · 4 hydrogen bonds · protein-protein
- G–K · 705 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 2A45 · Crystal structure of the complex between thrombin and the central "E" region of fibrin · the same entry in another collection · chain L against L, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P02671
- Every structure of UniProt P02675
- Every structure of UniProt P02679
- Elsewhere: RCSB PDB 2A45 · PDBe 2A45 · UniProt P00734 · UniProt P02671 · UniProt P02675 · UniProt P02679
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.