Research workbench
Crystal structure of ALPHA5BETA1 integrin headpiece in complex with rgd peptide
Analyse Crystal structure of ALPHA5BETA1 integrin headpiece in complex with rgd peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VI4
- Type
- protein
- Length
- 2,935 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-5; Integrin beta-1; SG/19 Fab fragment (light chain); SG/19 Fab fragment…
- UniProt
- P08648, P05556
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-5 | protein | 601 | 4% helix, 41% strand | P08648 |
| B | Integrin beta-1 | protein | 431 | 22% helix, 25% strand | P05556 |
| C | Integrin alpha-5 | protein | 589 | 4% helix, 37% strand | P08648 |
| D | Integrin beta-1 | protein | 433 | 23% helix, 27% strand | P05556 |
| L, E | SG/19 Fab fragment (light chain) | protein | 219 | 6% helix, 48% strand | — |
| H, F | SG/19 Fab fragment (heavy chain) | protein | 218 | 8% helix, 50% strand | — |
| G | Rgd peptide | protein | 4 | 0% helix, 0% strand | — |
| I | Rgd peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, C
- BMA · beta-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, I, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.80 | 0.87 | 66 | empty |
| 2 | 841 | 0.80 | 0.83 | 90 | empty |
| 3 | 471 | 0.68 | 0.79 | 61 | empty |
| 4 | 431 | 0.67 | 0.79 | 59 | empty |
| 5 | 142 | 0.67 | 0.88 | 38 | empty |
Interfaces
14 interfaces between chains.
- L–H · 1902 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1901 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1832 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 698 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 3VI4 · Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide · the same entry in another collection · chain I against I, TM-score 1.00
- P08648 · AlphaFold monomer V2.0 prediction for integrin alpha-5 (P08648) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P08648
- Every structure of UniProt P05556
- Elsewhere: RCSB PDB 3VI4 · PDBe 3VI4 · UniProt P08648 · UniProt P05556
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