MolNFT v1 · #13243 · protein
Crystal structure of the extracellular segment of integrin AVB3 in complex with an arg-gly-asp ligand
1L5G · Integrin alpha V: “Crystal structure of the extracellular segment of integrin AVB3 in complex with an arg-gly-asp ligand”. X-ray diffraction, 3 ligands (NAG, NDG, MN), 14 pockets (best druggability 0.81). MolNFT v1 #13243 on…
- PDB
- 1L5G
- Type
- protein
- Length
- 1,471 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha V; Integrin beta-3; Cyclic arg-gly-asp peptide
- UniProt
- P05106
- Ligands
- NAG, NDG, MN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha V | protein | 927 | 4% helix, 41% strand | — |
| B | Integrin beta-3 | protein | 539 | 17% helix, 25% strand | P05106 |
| C | Cyclic arg-gly-asp peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.81 | 0.82 | 97 | empty |
| 2 | 664 | 0.77 | 0.82 | 61 | empty |
| 3 | 531 | 0.66 | 0.77 | 42 | NAG |
| 4 | 183 | 0.46 | 0.75 | 29 | empty |
| 5 | 81 | 0.44 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2894 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 221 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 177 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 11 glycan, 1 modified (disulfide, N-glycosylation, methylation).
Compared structures
- 1L5G · Crystal structure of the extracellular segment of integrin AVB3 in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
- P05106 · AlphaFold monomer V2.0 prediction for integrin beta-3 (P05106) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P05106
- Elsewhere: RCSB PDB 1L5G · PDBe 1L5G · UniProt P05106
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