Research workbench
Crystal structure of A4B7 headpiece complexed with Fab act-1 and RO0505376
Analyse Crystal structure of A4B7 headpiece complexed with Fab act-1 and RO0505376 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V4V
- Type
- protein
- Length
- 2,770 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-4; Integrin beta-7; Monoclonal antibody act-1 heavy chain; Monoclonal…
- UniProt
- P13612, P26010
- Ligands
- 0DU, NAG, BMA, MAN, CA, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-4 | protein | 582 | 3% helix, 40% strand | P13612 |
| B, D | Integrin beta-7 | protein | 375 | 23% helix, 29% strand | P26010 |
| H | Monoclonal antibody act-1 heavy chain | protein | 211 | 3% helix, 56% strand | — |
| L, N | Monoclonal antibody act-1 light chain | protein | 217 | 4% helix, 47% strand | — |
| C | Integrin alpha-4 | protein | 580 | 4% helix, 40% strand | P13612 |
| M | Monoclonal antibody act-1 heavy chain | protein | 213 | 3% helix, 55% strand | — |
Ligands and binding sites
- 0DU · N-(2,6-dichlorobenzoyl)-4-[1,6-dimethyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl]-L-phenylalanine · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.83 | 0.88 | 72 | empty |
| 2 | 650 | 0.83 | 0.87 | 79 | empty |
| 3 | 1123 | 0.74 | 0.77 | 77 | empty |
| 4 | 690 | 0.66 | 0.75 | 91 | empty |
| 5 | 659 | 0.66 | 0.75 | 77 | empty |
Interfaces
13 interfaces between chains.
- M–N · 2057 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1993 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1564 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1553 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 531 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 3V4V · crystal structure of a4b7 headpiece complexed with Fab ACT-1 and RO0505376 · the same entry in another collection · chain N against N, TM-score 1.00
- P26010 · AlphaFold monomer V2.0 prediction for integrin beta-7 (P26010) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P13612 · AlphaFold monomer V2.0 prediction for integrin alpha-4 (P13612) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P13612
- Every structure of UniProt P26010
- Elsewhere: RCSB PDB 3V4V · PDBe 3V4V · UniProt P13612 · UniProt P26010
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