6AKX: Human Chemokine Receptor CCR5

The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Clostridium pasteurianum
Chains: 2
Atoms: 5,527
Mol. weight: 88.95 kDa
Ligands: A4R, ZN
Released: 24 Oct 2018

Explore 6AKX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AKX contains 40 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	26-53	28
α-helix	54-58	5
α-helix	64-81	18
α-helix	83-91	9
α-helix	98-131	34
α-helix	133-139	7
α-helix	142-166	25
β-strand	167-172	6	1
β-strand	175-180	6	1
α-helix	187-199	13
α-helix	200-204	5
α-helix	205-223	19
β-strand	1004-1006	3	2
β-strand	1012-1013	2	2
β-strand	1019	1	3
α-helix	1020-1022	3
β-strand	1024	1	3
α-helix	1030-1032	3
β-strand	1038	1	4
β-strand	1045	1	4
α-helix	1046-1048	3
β-strand	1049-1051	3	2
α-helix	1052-1054	3
α-helix	229-232	4
α-helix	234-259	26
α-helix	269-288	20
α-helix	289-291	3
α-helix	293-299	7
α-helix	302-308	7

Chain B: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	26-57	32
α-helix	64-80	17
α-helix	83-91	9
α-helix	98-131	34
α-helix	136-139	4
α-helix	142-165	24
β-strand	167-172	6	5
β-strand	175-180	6	5
α-helix	187-199	13
α-helix	200-204	5
α-helix	205-222	18
β-strand	1004-1006	3	6
β-strand	1012-1013	2	6
β-strand	1019	1	7
α-helix	1020-1022	3
β-strand	1024	1	7
α-helix	1030-1032	3
β-strand	1038	1	8
β-strand	1045	1	8
α-helix	1046-1048	3
β-strand	1049-1051	3	6
α-helix	1052-1053	2
α-helix	229-232	4
α-helix	234-259	26
α-helix	261-264	4
α-helix	269-288	20
α-helix	289-291	3
α-helix	293-299	7
α-helix	302-312	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5	A, B	protein	381	Homo sapiens, Clostridium pasteurianum	P00268 (AlphaFold model), P51681 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6AKX_1 C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5 (chains A, B)
GAPDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINY
KRLKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFF
IILLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPNIIFTRSQKEGLHYTC
SSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRMKKYTCTVCGYIYNP
EDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEEEKKRHRDVRLIFTIMIVYFLF
WAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFVGEEFRNY
LLVFFQKHIAKRGRPLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A4R	N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicy…	C26 H39 N5 O S	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (NO3) are not listed.

Primary citation

Structure-Based Design of 1-Heteroaryl-1,3-propanediamine Derivatives as a Novel Series of CC-Chemokine Receptor 5 Antagonists. Peng, P., Chen, H., Zhu, Y. et al. J Med Chem (2018) 61:9621-9636. DOI 10.1021/acs.jmedchem.8b01077 · PubMed

Other PDB entries of the same protein (UniProt P00268 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PVE 0.79 Å, NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of…
1IRO 1.1 Å, Rubredoxin (oxidized, fe(iii)) at 1.1 Å resolution
1IRN 1.2 Å, Rubredoxin (ZN-substituted) at 1.2 Å resolution
4RXN 1.2 Å, Crystallographic refinement of rubredoxin at 1.2 Å resolution
5RXN 1.2 Å, Combined crystallographic refinement and energy minimization of rubredoxin at 1.2 Å…
1SMM 1.36 Å, Crystal Structure of Cp Rd L41A mutant in oxidized state
1SMW 1.38 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked)
1SMU 1.43 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced)
1B13 1.5 Å, Clostridium pasteurianum rubredoxin G10A mutant
1FHH 1.5 Å, X-ray crystal structure of oxidized rubredoxin
1FHM 1.5 Å, X-ray crystal structure of reduced rubredoxin
1R0I 1.5 Å, cadmium-substituted rubredoxin

Browse structure collections

About this viewer

MolViewer shows 6AKX directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.