MolNFT v1 · #95495 · protein
Crystal structure of A4B7 headpiece complexed with Fab natalizumab
4IRZ · Integrin ALPHA4 subunit: “Crystal structure of A4B7 headpiece complexed with Fab natalizumab”. X-ray diffraction, 5 ligands (NDS, NAG, BMA), 11 pockets (best druggability 0.79). MolNFT v1 #95495 on GenesisL1: 3D structure, binding…
- PDB
- 4IRZ
- Type
- protein
- Length
- 1,017 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin ALPHA4 subunit; Fab natalizumab light chain; Fab natalizumab heavy chain
- Ligands
- NDS, NAG, BMA, CA, NA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin ALPHA4 subunit | protein | 592 | 4% helix, 40% strand | — |
| L | Fab natalizumab light chain | protein | 208 | 5% helix, 50% strand | — |
| H | Fab natalizumab heavy chain | protein | 217 | 6% helix, 56% strand | — |
Ligands and binding sites
- NDS · Ethyl dimethyl ammonio propane sulfonate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, H
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains H
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.79 | 0.85 | 66 | PEG, NDS |
| 2 | 544 | 0.71 | 0.80 | 45 | empty |
| 3 | 576 | 0.61 | 0.74 | 55 | empty |
| 4 | 180 | 0.53 | 0.79 | 23 | empty |
| 5 | 65 | 0.50 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1846 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 816 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 299 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4IRZ · Crystal structure of A4b7 headpiece complexed with Fab Natalizumab · 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
- Elsewhere: RCSB PDB 4IRZ · PDBe 4IRZ
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