MolNFT v1 · #115523 · protein

Oligomer crystal structure of cc chemokine 5 (CCL5)

5CMD · C-C motif chemokine 5: “Oligomer crystal structure of cc chemokine 5 (CCL5)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.69). MolNFT v1 #115523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CMD
Type: protein
Length: 383 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-C motif chemokine 5
UniProt: P13501
Ligands: SO4
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E	C-C motif chemokine 5	protein	64	22% helix, 28% strand	P13501
B	C-C motif chemokine 5	protein	64	20% helix, 28% strand	P13501
F	C-C motif chemokine 5	protein	63	19% helix, 30% strand	P13501

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, E, F

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.69	0.84	49	empty
2	296	0.63	0.80	39	empty
3	102	0.54	0.84	26	empty
4	86	0.51	0.83	26	empty
5	103	0.50	0.82	23	empty

Interfaces

9 interfaces between chains.

A–B · 650 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 647 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 629 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 625 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 576 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5CMD · Oligomer crystal structure of CC chemokine 5 (CCL5) · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.96

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 5CMD · PDBe 5CMD · UniProt P13501

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