Research workbench
Crystal structure of nerve growth factor in complex with lysophosphatidylinositol
Analyse Crystal structure of nerve growth factor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XPJ
- Type
- protein
- Length
- 210 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-nerve growth factor
- UniProt
- P01139
- Ligands
- LPY
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-nerve growth factor | protein | 105 | 0% helix, 64% strand | P01139 |
| B | Beta-nerve growth factor | protein | 105 | 0% helix, 65% strand | P01139 |
Ligands and binding sites
- LPY · (2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.61 | 0.80 | 34 | empty |
| 2 | 89 | 0.40 | 0.77 | 23 | empty |
| 3 | 61 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1254 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4XPJ · Crystal structure of Nerve growth factor in complex with lysophosphatidylinositol · the same entry in another collection · chain A against A, TM-score 1.00
- P01139 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01139) · a predicted model of the same protein · chain A 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 P01139
- Elsewhere: RCSB PDB 4XPJ · PDBe 4XPJ · UniProt P01139
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