7NJZ: Antibody RoAb13 Heavy Chain

X-ray crystallography study of RoAb13 which binds to PIYDIN, a part of the CCR5 N terminal domain. Determined by X-ray diffraction at 3.2 Å resolution. Released 21 Jul 2021.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,346
Mol. weight: 49.26 kDa
Released: 21 Jul 2021

Explore 7NJZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NJZ contains 13 α-helices and 46 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 H: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-83	7	1
α-helix	87-89	3
β-strand	91-98	8	2
β-strand	106-109	4	2
β-strand	113-117	5	2
β-strand	126-130	5	3
β-strand	143-151	9	3
β-strand	157-160	4	4
α-helix	171	1
β-strand	172	1	3
α-helix	173-174	2
β-strand	177	1	5
β-strand	180	1	5
β-strand	181-188	8	3
β-strand	200-205	6	4
β-strand	210-215	6	4
α-helix	218-220	3

Chain L: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	6
β-strand	12-14	3	7
β-strand	19-25	7	6
β-strand	30-31	2	8
β-strand	36-37	2	8
β-strand	39-44	6	9
β-strand	51-52	2	9
β-strand	54-55	2	10
β-strand	59-60	2	10
α-helix	61	1
β-strand	68-73	6	6
β-strand	76-81	6	6
β-strand	91-96	6	9
β-strand	104	1	9
β-strand	108-109	2	9
β-strand	111-113	3	7
α-helix	118-119	2
β-strand	120-124	5	11
α-helix	125-127	3
α-helix	128-132	5
β-strand	136-145	10	11
β-strand	151-152	2	12
β-strand	165	1	11
β-strand	168-169	2	11
α-helix	170-173	4
β-strand	179-182	4	11
β-strand	184-187	4	11
α-helix	189-193	5
β-strand	198	1	13
β-strand	201-203	3	12
β-strand	211-212	2	12
β-strand	215	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody RoAb13 Heavy Chain	H	protein	224	Mus musculus
Antibody RoAb13 Light Chain	L	protein	220	Mus musculus
Region from C-C chemokine receptor type 5 N-terminal domain	C	protein	6	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7NJZ_1 Antibody RoAb13 Heavy Chain (chains H)
EVQLQESGGGLVKPGGSLKLSCAASGFTFSTYAMSWVRQTPEKRLEWVASISTGDNTYYT
DSVRGRFTISRDNARNILYLQMSSLRSEDTAMYFCTRGRGDRGDLFGYWGQGTLVTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIK

Sequence of entity 2 (L), FASTA

>7NJZ_2 Antibody RoAb13 Light Chain (chains L)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYRGNQMNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTEFTLTISSVKAEDLTVYYCQQYYTYPRTFGGGTKLEIKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC

Sequence of entity 3 (C), FASTA

>7NJZ_3 Region from C-C chemokine receptor type 5 N-terminal domain (chains C)
PIYDIN

Primary citation

X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5. Govada, L., Saridakis, E., Kassen, S.C. et al. IUCrJ (2021) 8:678-683. DOI 10.1107/S2052252521005340 · PubMed

Other PDB entries of the same protein (UniProt P51681 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YD3 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide
5YD4 1.35 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)
5YY4 1.59 Å, Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide
9J8A 1.75 Å, Structure of antibody BA8 in complex with sulfated peptide from CCR5
5YD5 1.96 Å, Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)
5UIW 2.2 Å, Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV…
7F1T 2.6 Å, Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a
4MBS 2.71 Å, Crystal Structure of the CCR5 Chemokine Receptor
6AKX 2.8 Å, The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21
6AKY 2.8 Å, The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34
7F1S 2.8 Å, Cryo-EM structure of the apo chemokine receptor CCR5 in complex with Gi
7F1Q 2.9 Å, Cryo-EM structure of the chemokine receptor CCR5 in complex with MIP-1a and Gi

Browse structure collections

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