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Crystal structure of monomer Y60W hcrbpii

Analyse Crystal structure of monomer Y60W hcrbpii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZGU
Type: protein
Length: 532 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinol-binding protein 2
UniProt: P50120
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Retinol-binding protein 2	protein	133	8% helix, 56% strand	P50120

Ligands and binding sites

ACT · Acetate ion · additive · 8 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.84	0.91	56	ACT
2	191	0.79	0.93	29	ACT
3	339	0.78	0.89	47	ACT
4	267	0.77	0.89	40	ACT
5	406	0.65	0.79	45	empty

Interfaces

5 interfaces between chains.

A–D · 551 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 484 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 456 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 440 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 230 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4ZGU · Crystal structure of monomer Y60W hCRBPII · the same entry in another collection · chain A against A, TM-score 1.00
P50120 · AlphaFold monomer V2.0 prediction for retinol-binding protein 2 (P50120) · 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 P50120
Elsewhere: RCSB PDB 4ZGU · PDBe 4ZGU · UniProt P50120

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