9AVO: Engineered Protein GD with Human Kappa Fab

The crystal structure of an engineered Protein GD with Human Kappa Fab. Determined by X-ray diffraction at 3.0 Å resolution. Released 5 Feb 2025.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Streptococcus sp. 'group G'
Chains: 4
Atoms: 4,912
Mol. weight: 73.21 kDa
Released: 5 Feb 2025

Explore 9AVO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AVO contains 21 α-helices and 62 β-strands across 4 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: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	13
β-strand	19-20	2	14
α-helix	24	1
β-strand	25-33	9	13
β-strand	41-50	10	14
β-strand	55-65	11	14
β-strand	71-79	9	13
α-helix	80-82	3
α-helix	89-93	5
β-strand	95-104	10	14
β-strand	107-120	14	14
α-helix	123-127	5
α-helix	135-137	3
β-strand	138-151	14	14

Chain B: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
β-strand	12-13	2	2
β-strand	19-26	8	1
α-helix	30-32	3
β-strand	35-40	6	3
β-strand	46-53	8	3
β-strand	57-61	5	3
α-helix	63-65	3
β-strand	66	1	1
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-101	9	3
β-strand	104-108	5	3
β-strand	112-114	3	3
β-strand	115-116	2	2
α-helix	120-121	2
β-strand	122	1	4
β-strand	125-129	5	5
β-strand	137	1	5
β-strand	140-150	11	5
β-strand	151	1	4
α-helix	154	1
β-strand	156-159	4	6
α-helix	160-162	3
β-strand	164	1	6
β-strand	168-170	3	5
α-helix	171-173	3
β-strand	174-175	2	5
β-strand	181-190	10	5
α-helix	193-196	4
β-strand	200-205	6	6
β-strand	210-215	6	6

Chain C: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	6
β-strand	18-25	8	6
α-helix	28-36	9
β-strand	49-51	3	6
β-strand	56-60	5	6

Chain D: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	5-7	3	8
β-strand	10-13	4	9
β-strand	19-24	6	8
α-helix	30-32	3
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-91	7	9
β-strand	96-98	3	9
β-strand	99	1	7
β-strand	102-106	5	9
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	122-127	6
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	144-150	7	12
β-strand	153-155	3	12
β-strand	159-160	2	11
β-strand	163	1	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-198	8	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Heavy Chain	B	protein	228	Homo sapiens
Fab Light Chain	D	protein	215	Homo sapiens
Histone chaperone ASF1	A	protein	164	Homo sapiens	P32447 (AlphaFold model)
Protein GD	C	protein	65	Streptococcus sp. 'group G'	P19909 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9AVO_1 Fab Heavy Chain (chains B)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSYYSIHWVRQAPGKGLEWVASIYPYYGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYGWALDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (D), FASTA

>9AVO_2 Fab Light Chain (chains D)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQDGWSLITFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>9AVO_3 Histone chaperone ASF1 (chains A)
QGSSSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQEL
DSILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEY
DEEELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGLE

Sequence of entity 4 (C), FASTA

>9AVO_4 Protein GD (chains C)
TPAVTTYKLVINGRTLSGYTTTTAVDAATAEKVFKQIDMVSSVDGEWTYDDATKTFTVTE
KPEKL

Primary citation

Engineered protein G variants for multifunctional antibody-based assemblies. Slezak, T., O'Leary, K.M., Li, J. et al. Protein Sci (2025) 34:e70019-e70019. DOI 10.1002/pro.70019 · PubMed

Other PDB entries of the same protein (UniProt P32447 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ROC 1.5 Å, Crystal structure of the histone deposition protein Asf1
5UCB 1.52 Å, Structure of antigen-Fab complex with engineered switch residue region.
2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
5UEK 1.7 Å, Structure of antigen-Fab 12E complex with Histone chaperone ASF1
5UEA 1.7 Å, Structure of antigen-Fab complex with Histone chaperone ASF1
6AYZ 2.1 Å, Crystal structure of Asf1-Fab 12E complex
2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
4ZBJ 2.25 Å, UBN1 peptide bound to H3.3/H4/Asf1
4EO5 2.35 Å, Yeast Asf1 bound to H3/H4G94P mutant
5EII 2.44 Å, Structural determination of an protein complex of a Fab with increased solubility
6AZ2 2.48 Å, Crystal structure of Asf1-Fab 12E complex
4RRP 2.79 Å, Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics…

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