MolNFT v1 · #63881 · protein
Crystal structure of retinol-binding protein 4 (RBP4) in complex with non-retinoid ligand
3FMZ: “Crystal structure of retinol-binding protein 4 (RBP4) in complex with non-retinoid ligand”. X-ray diffraction, 1 ligand (2T1), 5 pockets (best druggability 0.76). MolNFT v1 #63881 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3FMZ
- Type
- protein
- Length
- 348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 4
- UniProt
- P02753
- Ligands
- 2T1
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 4 | protein | 174 | 11% helix, 47% strand | P02753 |
Ligands and binding sites
- 2T1 · 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.76 | 0.90 | 34 | 2T1 |
| 2 | 205 | 0.75 | 0.90 | 33 | 2T1 |
| 3 | 515 | 0.64 | 0.77 | 46 | empty |
| 4 | 73 | 0.31 | 0.73 | 16 | empty |
| 5 | 58 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 182 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3FMZ · Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand · the same entry in another collection · chain A against A, TM-score 1.00
- P02753 · AlphaFold monomer V2.0 prediction for retinol-binding protein 4 (P02753) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P02753
- Elsewhere: RCSB PDB 3FMZ · PDBe 3FMZ · UniProt P02753
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