Research workbench
Crystal structure of A4B7 headpiece complexed with Fab act-1
Analyse Crystal structure of A4B7 headpiece complexed with Fab act-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V4P
- Type
- protein
- Length
- 2,769 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
- NAG, BMA, MAN, CA, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 40% 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 |
| C | Integrin alpha-4 | protein | 581 | 3% helix, 40% strand | P13612 |
| H, M | Monoclonal antibody act-1 heavy chain | protein | 211 | 1% helix, 54% strand | — |
| L, N | Monoclonal antibody act-1 light chain | protein | 217 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- 15P · Polyethylene glycol (N=34) · additive · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C, D
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 | 673 | 0.83 | 0.87 | 75 | empty |
| 2 | 649 | 0.83 | 0.87 | 74 | empty |
| 3 | 1044 | 0.73 | 0.76 | 75 | 15P |
| 4 | 420 | 0.61 | 0.76 | 56 | MG |
| 5 | 372 | 0.58 | 0.76 | 50 | MG |
Interfaces
12 interfaces between chains.
- H–L · 2062 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 2032 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1575 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1561 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 530 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3V4P · crystal structure of a4b7 headpiece complexed with Fab ACT-1 · 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 C against A, TM-score 0.93
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 3V4P · PDBe 3V4P · UniProt P13612 · UniProt P26010
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