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Crystal structure of avidin in complex with ferrocene homobiotin derivative

Analyse Crystal structure of avidin in complex with ferrocene homobiotin derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MYQ
Type: protein
Length: 488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: HBF, NAG, IOD
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Avidin	protein	122	5% helix, 50% strand	P02701

Ligands and binding sites

HBF · ferrocene homobiotin derivative · ligand · 4 copies · chains A, C, B, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
IOD · Iodide ion · ion · 21 copies · chains A, B, D, C

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

Pockets

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	185	0.65	0.84	25	HBF, IOD
2	174	0.63	0.84	25	HBF, IOD
3	210	0.63	0.82	29	HBF, IOD
4	189	0.61	0.82	31	HBF, IOD
5	117	0.58	0.85	23	empty

Interfaces

6 interfaces between chains.

C–D · 1974 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 1969 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 648 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 645 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 154 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5MYQ · Crystal structure of avidin in complex with ferrocene homobiotin derivative · the same entry in another collection · chain D against D, TM-score 1.00
P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 5MYQ · PDBe 5MYQ · UniProt P02701

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