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Crystal structure of cellular retinoic acid binding protein 2 (CRABP2)-aryl fluorosulfate covalent conjugate
Analyse Crystal structure of cellular retinoic acid binding protein 2 (CRABP2)-aryl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HZQ
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular retinoic acid-binding protein 2
- UniProt
- P29373
- Ligands
- YWZ
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular retinoic acid-binding protein 2 | protein | 139 | 14% helix, 53% strand | P29373 |
| B | Cellular retinoic acid-binding protein 2 | protein | 136 | 13% helix, 56% strand | P29373 |
Ligands and binding sites
- YWZ · 4'-[(3,6,9,12-tetraoxapentadec-14-yn-1-yl)oxy][1,1'-biphenyl]-4-yl sulfurofluoridate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.81 | 0.87 | 44 | YWZ, GOL |
| 2 | 485 | 0.80 | 0.87 | 48 | YWZ |
| 3 | 94 | 0.52 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 958 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5HZQ · Crystal structure of cellular retinoic acid binding protein 2 (CRABP2)-aryl fluorosulfate… · the same entry in another collection · chain A against A, TM-score 1.00
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 P29373
- Elsewhere: RCSB PDB 5HZQ · PDBe 5HZQ · UniProt P29373
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