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Human afamin orthorhombic crystal form by controlled hydration

Analyse Human afamin orthorhombic crystal form by controlled hydration in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FAK
Type: protein
Length: 575 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Afamin
UniProt: P43652
Ligands: NAG, NA, CL
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Afamin	protein	575	68% helix, 1% strand	P43652

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · chains A
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A
P6G · Hexaethylene glycol · additive · 2 copies · chains A
PG4 · Tetraethylene glycol · additive · 2 copies · chains A
PGE · Triethylene glycol · additive · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A
ACT · Acetate ion · additive · chains A
PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	494	0.78	0.85	52	PG4, PEG, PG6
2	409	0.73	0.83	54	CL
3	131	0.62	0.85	24	empty
4	198	0.56	0.79	30	empty
5	144	0.54	0.80	16	PGE

Modifications

Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6FAK · Human afamin orthorhombic crystal form by controlled hydration · the same entry in another collection · chain A against A, TM-score 1.00
P43652 · AlphaFold monomer V2.0 prediction for afamin (P43652) · 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 P43652
Elsewhere: RCSB PDB 6FAK · PDBe 6FAK · UniProt P43652

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