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Crystal structure of chemokine domain of fractalkine

Analyse Crystal structure of chemokine domain of fractalkine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F2L
Type: protein
Length: 262 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fractalkine
UniProt: P78423
Pockets: 4 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Fractalkine	protein	64	27% helix, 28% strand	P78423
D	Fractalkine	protein	70	33% helix, 26% strand	P78423

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.50	0.76	21	empty
2	202	0.49	0.76	24	empty
3	80	0.43	0.79	14	empty
4	91	0.42	0.78	15	empty

Interfaces

5 interfaces between chains.

A–D · 788 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 728 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 346 Å² buried · 1 hydrogen bond · protein-protein
A–B · 287 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 116 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1F2L · Crystal structure of chemokine domain of fractalkine · the same entry in another collection · chain A against A, TM-score 1.00
P78423 · AlphaFold monomer V2.0 prediction for fractalkine (P78423) · a predicted model of the same protein · chain D against A, TM-score 0.88

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 P78423
Elsewhere: RCSB PDB 1F2L · PDBe 1F2L · UniProt P78423

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