7DOH: GD-26 Fab

Crystal Structure of GD-26 Fab in Complex with TD Peptide from Haloarcula Marismortui Bacteriorhodopsin I. Determined by X-ray diffraction at 1.45 Å resolution. Released 27 Oct 2021.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Haloarcula marismortui, Mus musculus
Chains: 3
Atoms: 4,143
Mol. weight: 49.6 kDa
Released: 27 Oct 2021

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

Secondary structure: helices and β-sheets

7DOH contains 18 α-helices and 45 β-strands across 3 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	17-25	9	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-52	8	8
β-strand	57-60	4	8
α-helix	62-65	4
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-84	7	7
α-helix	88-90	3
β-strand	92-98	7	8
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-171	3	10
β-strand	174-184	11	10
β-strand	194-199	6	11
α-helix	200-202	3
β-strand	204-209	6	11

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30	1	3
β-strand	36	1	3
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-95	7	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	116	1	4
α-helix	117-118	2
β-strand	119-123	5	5
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	5
β-strand	145	1	4
β-strand	150-155	6	6
β-strand	158-160	3	6
β-strand	164-168	5	5
α-helix	169-172	4
β-strand	178-187	10	5
α-helix	188-191	4
β-strand	196-202	7	6
β-strand	210-215	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gly-thr-gly-ala-thr-pro-ala-asp-asp	I	protein	9	Haloarcula marismortui	Q5UXY6 (AlphaFold model)
GD-26 Fab L-chain	L	protein	219	Mus musculus
GD-26 Fab H-chain	H	protein	227	Mus musculus

Sequence of entity 1 (I), FASTA

>7DOH_1 GLY-THR-GLY-ALA-THR-PRO-ALA-ASP-ASP (chains I)
GTGATPADD

Sequence of entity 2 (L), FASTA

>7DOH_2 GD-26 Fab L-chain (chains L)
DVVLTQTPLSLSVTIGQPASISCRSSQRLLYSNGKTYLNWFQQRPGQAPKYLMFQVSKLG
PGIPARFSGSGSETDFTLKISRVEAEDLGVYYCFQGTFFPHTFGGGTKLEMKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>7DOH_3 GD-26 Fab H-chain (chains H)
QVQLRQSGPELVKPGASVKMSCRASGYTFTNYNIHWVRQRPGQGLEWIGWIYPVDGTTKY
NEKFKDKTTLTSDKSSSTAYMSLSGLTSEDSAIYFCARGLDNWGQGTSVTVSSAKTTAPS
VYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPGSHHHHHH

Primary citation

Structural basis of an epitope tagging system derived from Haloarcula marismortui bacteriorhodopsin I D94N and its monoclonal antibody GD-26. Pao, P.J., Hsu, M.F., Chiang, M.H. et al. FEBS J (2022) 289:730-747. DOI 10.1111/febs.16184 · PubMed

Other PDB entries of the same protein (UniProt Q5UXY6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PXK 2.5 Å, Crystal structure of Haloarcula marismortui bacteriorhodopsin I D94N mutant
8Y9Z 3.41 Å, Structure of the SecA-SecY complex with the substrate HmBRI-3TM

Browse structure collections

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