MolNFT v1 · #115368 · protein

Crystal structure of avidin - haba complex (hexagonal crystal form)

5CHK: “Crystal structure of avidin - haba complex (hexagonal crystal form)”. X-ray diffraction, 2 ligands (55R, NAG), 1 pocket (best druggability 0.46). MolNFT v1 #115368 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CHK
Type: protein
Length: 121 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: 55R, NAG
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Avidin	protein	121	5% helix, 52% strand	P02701

Ligands and binding sites

55R · 2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.46	0.78	19	55R

Modifications

Observed in the structure: 1 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5CHK · Crystal structure of avidin - HABA complex (hexagonal crystal form) · the same entry in another collection · chain A against A, TM-score 1.00
P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P02701
Elsewhere: RCSB PDB 5CHK · PDBe 5CHK · UniProt P02701

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