MolNFT v1 · #112407 · protein

The chemokine binding protein of orf virus complexed with CCL7

4ZKC: “The chemokine binding protein of orf virus complexed with CCL7”. X-ray diffraction, 2 ligands (NAG, BMA), 2 pockets (best druggability 0.68). MolNFT v1 #112407 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ZKC
Type: protein
Length: 277 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chemokine binding protein; C-C motif chemokine 7
UniProt: Q2F862, P80098
Ligands: NAG, BMA
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chemokine binding protein	protein	217	14% helix, 44% strand	Q2F862
B	C-C motif chemokine 7	protein	60	17% helix, 27% strand	P80098

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
BMA · beta-D-mannopyranose · sugar · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	377	0.68	0.81	62	empty
2	57	0.30	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 700 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4ZKC · The chemokine binding protein of orf virus complexed with CCL7 · the same entry in another collection · chain A against A, TM-score 1.00
P80098 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 7 (P80098) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 Q2F862
Every structure of UniProt P80098
Elsewhere: RCSB PDB 4ZKC · PDBe 4ZKC · UniProt Q2F862 · UniProt P80098

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