MolNFT v1 · #117443 · protein
Crystal structure of thrombin bound to an exosite 1-specific IgA Fab
5E8E · IgA Fab light chain: “Crystal structure of thrombin bound to an exosite 1-specific IgA Fab”. X-ray diffraction, 8 ligands (0G6, NAG, BMA), 6 pockets (best druggability 0.59). MolNFT v1 #117443 on GenesisL1: 3D structure, binding…
- PDB
- 5E8E
- Type
- protein
- Length
- 736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgA Fab light chain; IgA Fab heavy chain; Thrombin heavy chain; Thrombin light chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, BMA, MAN, GAL, SIA, NA, PO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgA Fab light chain | protein | 215 | 7% helix, 51% strand | — |
| B | IgA Fab heavy chain | protein | 229 | 5% helix, 49% strand | — |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 259 | 14% helix, 34% strand | P00734 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 33 | 30% helix, 0% strand | P00734 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, H
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar
- NA · Sodium ion · metal · chains H
- PO4 · Phosphate ion · ion · 5 copies · chains B, H
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, H, L
- CIT · Citric acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.59 | 0.78 | 42 | PO4, 0G6 |
| 2 | 242 | 0.59 | 0.79 | 39 | empty |
| 3 | 365 | 0.56 | 0.74 | 45 | PEG |
| 4 | 118 | 0.38 | 0.74 | 21 | empty |
| 5 | 111 | 0.36 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1953 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1407 Ų buried · 33 hydrogen bonds · protein-protein
- B–H · 576 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 covalent, 2 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, cyclization).
Compared structures
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 5E8E · PDBe 5E8E · UniProt P00734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.