7NW3: Antibody RoAb13 Heavy Chain

X-ray crystallographic study of PIYDIN, which contains the truncation determinants of binding PI and N, bound to RoAb13, a CCR5 antibody. 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: 3,331
Mol. weight: 49.26 kDa
Released: 21 Jul 2021

Explore 7NW3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NW3 contains 12 α-helices and 48 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: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-11	2	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	91-97	7	2
β-strand	108-109	2	2
β-strand	113-116	4	2
α-helix	120-122	3
β-strand	123	1	3
α-helix	124-126	3
β-strand	128-130	3	4
β-strand	141-147	7	4
β-strand	148-149	2	5
β-strand	152	1	3
β-strand	157-160	4	6
β-strand	170-171	2	4
β-strand	175-177	3	5
β-strand	180-183	4	5
β-strand	185-190	6	4
β-strand	199-205	7	6
β-strand	210-216	7	6

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	7
β-strand	12-13	2	8
β-strand	19-25	7	7
β-strand	30-31	2	9
β-strand	36-37	2	9
β-strand	39-44	6	10
β-strand	51-55	5	10
β-strand	59-60	2	10
α-helix	61	1
β-strand	68-73	6	7
β-strand	76-81	6	7
β-strand	91-96	6	10
α-helix	102	1
β-strand	103-104	2	10
β-strand	108-109	2	10
β-strand	111-112	2	8
β-strand	120	1	11
β-strand	123-124	2	12
α-helix	125-127	3
α-helix	130-133	4
β-strand	136-138	3	13
β-strand	139-140	2	12
β-strand	142-145	4	11
β-strand	152	1	14
β-strand	169	1	11
α-helix	170-173	4
β-strand	179-181	3	11
β-strand	185-187	3	13
α-helix	190-192	3
β-strand	197-202	6	14
β-strand	211-216	6	14

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	A	protein	6	Homo sapiens	P51681 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7NW3_1 Antibody RoAb13 Heavy Chain (chains H)
EVQLQESGGGLVKPGGSLKLSCAASGFTFSTYAMSWVRQTPEKRLEWVASISTGDNTYYT
DSVRGRFTISRDNARNILYLQMSSLRSEDTAMYFCTRGRGDRGDLFGYWGQGTLVTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIK

Sequence of entity 2 (L), FASTA

>7NW3_2 Antibody RoAb13 Light Chain (chains L)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYRGNQMNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTEFTLTISSVKAEDLTVYYCQQYYTYPRTFGGGTKLEIKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC

Sequence of entity 3 (A), FASTA

>7NW3_3 Region from C-C chemokine receptor type 5 N-terminal domain (chains A)
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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