MolNFT v1 · #51252 · protein
Crystal structure of human lim protein ril (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1
2V1W · PDZ and lim domain protein 4: “Crystal structure of human lim protein ril (PDLIM4) PDZ domain bound to the C-terminal peptide of human…”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.38). MolNFT v1 #51252 on…
- PDB
- 2V1W
- Type
- protein
- Length
- 179 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PDZ and lim domain protein 4
- UniProt
- P50479
- Ligands
- MG
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PDZ and lim domain protein 4 | protein | 89 | 18% helix, 38% strand | P50479 |
| B | PDZ and lim domain protein 4 | protein | 90 | 17% helix, 38% strand | P50479 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · chains A, B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.38 | 0.78 | 24 | empty |
| 2 | 53 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 493 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2V1W · Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal… · the same entry in another collection · chain A against A, TM-score 1.00
- P50479 · AlphaFold monomer V2.0 prediction for PDZ and lim domain protein 4 (P50479) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P50479
- Elsewhere: RCSB PDB 2V1W · PDBe 2V1W · UniProt P50479
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