6CBJ: DH270.3 Fab

Crystal Structure of DH270.3 Fab in complex with Man9. Determined by X-ray diffraction at 2.85 Å resolution. Released 21 Feb 2018.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,396
Mol. weight: 50.53 kDa
Ligands: PO4
Released: 21 Feb 2018

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

Secondary structure: helices and β-sheets

6CBJ contains 21 α-helices and 47 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: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	45-51	7	2
β-strand	58-59	2	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-101	10	2
α-helix	102	1
β-strand	116-117	2	2
β-strand	118	1	1
β-strand	121-125	5	2
α-helix	129-130	2
β-strand	131	1	3
α-helix	132-133	2
β-strand	134-138	5	4
β-strand	149-159	11	4
β-strand	160	1	3
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	173	1	5
β-strand	177-179	3	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-199	10	4
α-helix	200-202	3
α-helix	207	1
β-strand	208-214	7	5
α-helix	215-217	3
β-strand	219-225	7	5

Chain L: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	5	1	7
β-strand	9-12	4	8
β-strand	18-23	6	7
β-strand	35-40	6	8
α-helix	45-46	2
β-strand	47-51	5	8
β-strand	55-56	2	8
α-helix	57	1
β-strand	64-69	6	7
β-strand	72-77	6	7
α-helix	82-84	3
β-strand	87-93	7	8
β-strand	99-101	3	8
β-strand	102	1	6
β-strand	105-109	5	8
α-helix	112-114	3
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-159	3	11
β-strand	165	1	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-184	9	10
α-helix	186-190	5
β-strand	195-201	7	11
β-strand	204-210	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DH270.3 Fab heavy chain	H	protein	238	Homo sapiens	S6C4S0 (AlphaFold model)
DH270.3 Fab light chain	L	protein	216	Homo sapiens	Q6PJG0 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6CBJ_1 DH270.3 Fab heavy chain (chains H)
QVQLVQSGAELKKPGASVKVSCKASGYTLSDYYVHWLRQAPGQGLEWVAWINPTSGRTIS
PRKFQGRVTMTTDTSMNVAYMELRGLRSDDTAVYFCARGGWISLYVDYSYYPNFDSWGQG
TLVSVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Sequence of entity 2 (L), FASTA

>6CBJ_2 DH270.3 Fab light chain (chains L)
QPVLTQPASVSGSPGQSITISCTGSSSDVGSYNLVSWYQQHPGKAPKLMIYEVNKWASGV
SDRFAGSKSGNTASLTISRLQAEDEANYFCSSSTNSATVIFGGGTKLTVLGQPKGAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Primary citation

HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope. Fera, D., Lee, M.S., Wiehe, K. et al. Nat Commun (2018) 9:1111-1111. DOI 10.1038/s41467-018-03565-6 · PubMed

Other PDB entries of the same protein (UniProt S6C4S0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W08 2.6 Å, A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab
4NM4 2.65 Å, Crystal structure of broadly neutralizing antibody CR8043
4O58 2.75 Å, Crystal structure of broadly neutralizing antibody F045-092 in complex with…
5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody
6UTA 3.1 Å, Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
4NM8 4.0 Å, Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza…
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…
4O5I 6.5 Å, Crystal structure of broadly neutralizing antibody F045-092 in complex with…

Browse structure collections

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