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Structure of CXCL12:HEPARIN disaccharide complex

Analyse Structure of CXCL12:HEPARIN disaccharide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NWG
Type: protein
Length: 132 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stromal cell-derived factor 1
UniProt: P48061
Ligands: UAP, SGN
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stromal cell-derived factor 1	protein	68	18% helix, 25% strand	P48061
B	Stromal cell-derived factor 1	protein	64	22% helix, 27% strand	P48061

Ligands and binding sites

UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A, B

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	52	0.32	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 987 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2NWG · Structure of CXCL12:heparin disaccharide complex · the same entry in another collection · chain A against A, TM-score 1.00
P48061 · AlphaFold monomer V2.0 prediction for stromal cell-derived factor 1 (P48061) · a predicted model of the same protein · chain B against A, TM-score 0.84

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 P48061
Elsewhere: RCSB PDB 2NWG · PDBe 2NWG · UniProt P48061

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