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The crystal structure of apo domain-swapped dimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H variant of hcrbpii

Analyse The crystal structure of apo domain-swapped dimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WNF
Type: protein
Length: 266 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinol-binding protein 2
UniProt: P50120
Pockets: 1 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Retinol-binding protein 2	protein	133	11% helix, 58% strand	P50120

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains A, B
ACT · Acetate ion · additive · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.87	0.88	99	GOL

Interfaces

1 interface between chains.

A–B · 3783 Å² buried · 68 hydrogen bonds · protein-protein

Compared structures

6WNF · The Crystal Structure of Apo Domain-Swapped Dimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H… · the same entry in another collection · chain A against A, TM-score 1.00

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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 6WNF · PDBe 6WNF · UniProt P50120

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