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Crystal structure of human CCL5 trimer

Analyse Crystal structure of human CCL5 trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AEZ
Type: protein
Length: 195 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-C motif chemokine 5
UniProt: P13501
Ligands: SO4
Pockets: 1 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-C motif chemokine 5	protein	64	17% helix, 30% strand	P13501
B	C-C motif chemokine 5	protein	64	19% helix, 33% strand	P13501
C	C-C motif chemokine 5	protein	67	19% helix, 27% strand	P13501

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C

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	78	0.41	0.79	23	empty

Interfaces

3 interfaces between chains.

B–C · 779 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 455 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 132 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6AEZ · Crystal structure of human CCL5 trimer · the same entry in another collection · chain A against A, TM-score 1.00
P13501 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 5 (P13501) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P13501
Elsewhere: RCSB PDB 6AEZ · PDBe 6AEZ · UniProt P13501

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