MolNFT v1 · #125229 · protein

Oligomer crystal structure of cc chemokine 5 (CCL5)

5L2U · C-C motif chemokine 5: “Oligomer crystal structure of cc chemokine 5 (CCL5)”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.57). MolNFT v1 #125229 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L2U
Type: protein
Length: 581 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-C motif chemokine 5
UniProt: P13501
Ligands: CL
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, I	C-C motif chemokine 5	protein	65	22% helix, 29% strand	P13501
D, F, G, H	C-C motif chemokine 5	protein	64	23% helix, 28% strand	P13501

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, F
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, G, F
GOL · Glycerol · additive · 2 copies · chains A, G

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

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	250	0.57	0.78	26	empty
2	246	0.55	0.77	31	empty
3	181	0.46	0.75	22	empty

Interfaces

13 interfaces between chains.

A–B · 768 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 716 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 705 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 694 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 626 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

5L2U · Oligomer crystal structure of CC chemokine 5 (CCL5) · the same entry in another collection · chain I against I, 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 F against A, TM-score 0.97

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 5L2U · PDBe 5L2U · UniProt P13501

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