3ODU: PDB entry 3ODU

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Oct 2010.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo Sapiens, Enterobacteria phage T4
Chains: 2
Atoms: 7,805
Mol. weight: 118.22 kDa
Ligands: ITD, OLA, OLC
Released: 27 Oct 2010

Explore 3ODU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ODU contains 57 α-helices and 16 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: 30 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	37-61	25
α-helix	62-66	5
α-helix	72-88	17
α-helix	91-99	9
α-helix	105-139	35
α-helix	145-150	6
α-helix	151-155	5
α-helix	156	1
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-174	6
β-strand	175-179	5	1
β-strand	184-188	5	1
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-225	16
α-helix	226-228	3
α-helix	1003-1010	8
β-strand	1014-1015	2	2
β-strand	1016	1	3
β-strand	1017-1019	3	2
β-strand	1025-1028	4	2
β-strand	1031-1034	4	2
α-helix	1039-1050	12
β-strand	1057	1	3
α-helix	1060-1078	19
α-helix	1085-1089	5
α-helix	1093-1112	20
α-helix	1115-1123	9
α-helix	1126-1133	8
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1159-1200	4
α-helix	231-266	36
α-helix	274-291	18
α-helix	294-301	8
α-helix	313-317	5
α-helix	324-326	3

Chain B: 27 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	34-38	5
α-helix	39-61	23
α-helix	62-66	5
α-helix	72-88	17
α-helix	91-99	9
α-helix	105-139	35
α-helix	145-150	6
α-helix	151-155	5
α-helix	156	1
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-174	6
β-strand	175-180	6	4
β-strand	183-188	6	4
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-225	16
α-helix	1002-1011	10
β-strand	1014-1015	2	5
β-strand	1016	1	6
β-strand	1017-1019	3	5
β-strand	1025-1028	4	5
β-strand	1031-1032	2	5
α-helix	1039-1050	12
β-strand	1057	1	6
α-helix	1060-1078	19
α-helix	1085-1090	6
α-helix	1093-1112	20
α-helix	1115-1122	8
α-helix	1126-1133	8
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	231-266	36
α-helix	274-291	18
α-helix	294-301	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-X-C chemokine receptor type 4, Lysozyme Chimera	A, B	protein	502	Homo Sapiens, Enterobacteria phage T4	P00720, P61073 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3ODU_1 C-X-C chemokine receptor type 4, Lysozyme Chimera (chains A, B)
DYKDDDDAGAPEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFL
TGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCK
AVHVIYTVNLYSSVWILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIP
DFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSG
SNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITK
DEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRM
LQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSKGHQKRKALKTTVILIL
AFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLG
AKFKTSAQHALTSGRPLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
ITD	(6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl…	C21 H34 N4 S2	2
OLA	Oleic acid	C18 H34 O2	6
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	5

Primary citation

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Wu, B., Chien, E.Y., Mol, C.D. et al. Science (2010) 330:1066-1071. DOI 10.1126/science.1194396 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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3ODU is part of these collections:

GPCRs and cell signaling

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