MolNFT v1 · #111848 · protein

Crystal structure of short hoefavidin-hoef-peptide complex

4Z2V · Avidin family: “Crystal structure of short hoefavidin-hoef-peptide complex”. X-ray diffraction, 3 pockets (best druggability 0.50). MolNFT v1 #111848 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z2V
Type: protein
Length: 274 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin family; Hoef-peptide
UniProt: A9D857
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Avidin family	protein	127	6% helix, 61% strand	A9D857
P	Hoef-peptide	protein	10	0% helix, 20% strand	—
B	Avidin family	protein	126	4% helix, 60% strand	A9D857
C	Hoef-peptide	protein	11	0% helix, 18% strand	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.50	0.78	35	empty
2	75	0.50	0.84	19	empty
3	76	0.50	0.83	17	empty

Interfaces

4 interfaces between chains.

A–B · 1642 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 564 Å² buried · 10 hydrogen bonds · protein-protein
A–P · 561 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 13 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4Z2V · Crystal structure of short hoefavidin-hoef-peptide complex · the same entry in another collection · chain A against A, TM-score 1.00
A9D857 · AlphaFold monomer V2.0 prediction for hoefavidin (A9D857) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 A9D857
Elsewhere: RCSB PDB 4Z2V · PDBe 4Z2V · UniProt A9D857

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