Research workbench
Crystal structure of integrin binding fragment of laminin-511
Analyse Crystal structure of integrin binding fragment of laminin-511 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XAU
- Type
- protein
- Length
- 1,459 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laminin subunit alpha-5; Laminin subunit beta-1; Laminin subunit gamma-1
- UniProt
- O15230, P07942, P11047
- Ligands
- NAG, CA
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laminin subunit alpha-5 | protein | 600 | 13% helix, 44% strand | O15230 |
| B | Laminin subunit beta-1 | protein | 71 | 96% helix, 0% strand | P07942 |
| C | Laminin subunit gamma-1 | protein | 70 | 84% helix, 0% strand | P11047 |
| D | Laminin subunit alpha-5 | protein | 594 | 15% helix, 43% strand | O15230 |
| E | Laminin subunit beta-1 | protein | 72 | 94% helix, 0% strand | P07942 |
| F | Laminin subunit gamma-1 | protein | 52 | 81% helix, 0% strand | P11047 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, D
- CA · Calcium ion · metal · 2 copies · chains A, D
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 | 1138 | 0.87 | 0.88 | 166 | empty |
| 2 | 979 | 0.79 | 0.81 | 107 | empty |
| 3 | 324 | 0.59 | 0.77 | 36 | empty |
| 4 | 87 | 0.57 | 0.87 | 32 | empty |
| 5 | 172 | 0.45 | 0.75 | 22 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1829 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1552 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1415 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1385 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1224 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5XAU · Crystal structure of integrin binding fragment of laminin-511 · the same entry in another collection · chain F against F, TM-score 1.00
- P11047 · AlphaFold monomer V2.0 prediction for laminin subunit gamma-1 (P11047) · a predicted model of the same protein · chain F against A, TM-score 0.81
- P07942 · AlphaFold monomer V2.0 prediction for laminin subunit beta-1 (P07942) · a predicted model of the same protein · chain B against A, TM-score 0.74
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 O15230
- Every structure of UniProt P07942
- Every structure of UniProt P11047
- Elsewhere: RCSB PDB 5XAU · PDBe 5XAU · UniProt O15230 · UniProt P07942 · UniProt P11047
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