6T9E: Bispecific DutaFab

Crystal structure of a bispecific DutaFab in complex with human PDGF. Determined by X-ray diffraction at 2.99 Å resolution. Released 16 Dec 2020.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,935
Mol. weight: 119.48 kDa
Released: 16 Dec 2020

Explore 6T9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T9E contains 34 α-helices and 101 β-strands across 6 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 AAA: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	11-12	2	2
β-strand	17-23	7	1
α-helix	27-31	5
β-strand	33-39	7	3
β-strand	46-51	6	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	106	1	3
β-strand	110-112	3	3
β-strand	113-114	2	2
β-strand	120	1	4
α-helix	121-122	2
β-strand	123-127	5	5
β-strand	139-148	10	5
β-strand	149	1	4
β-strand	154-157	4	6
α-helix	158-160	3
β-strand	162	1	6
β-strand	166-168	3	5
α-helix	169-171	3
β-strand	172-173	2	5
β-strand	179-187	9	5
β-strand	198-203	6	6
α-helix	204-206	3
β-strand	208-213	6	6

Chain BBB: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-7	3	7
β-strand	10-14	5	8
β-strand	19-24	6	7
β-strand	33-38	6	8
β-strand	44-49	6	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-107	6	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-148	4	11
β-strand	155	1	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	194-197	4	11
β-strand	205-207	3	11

Chain CCC: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	12
β-strand	17-24	8	13
β-strand	37-40	4	14
β-strand	43-50	8	13
β-strand	59-78	20	14
β-strand	81-100	20	14

Chain DDD: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	14
β-strand	17-24	8	15
β-strand	37-40	4	12
β-strand	43-50	8	15
β-strand	58-78	21	12
β-strand	81-101	21	12

Chain HHH: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	11-12	2	17
β-strand	17-23	7	16
α-helix	27-31	5
β-strand	33-39	7	18
β-strand	46-51	6	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	16
β-strand	78-84	7	16
α-helix	88-90	3
β-strand	92-99	8	18
β-strand	106	1	18
β-strand	110-112	3	18
β-strand	113-114	2	17
β-strand	120	1	19
α-helix	121-122	2
β-strand	123-127	5	20
β-strand	130	1	21
α-helix	131-134	4
β-strand	138-148	11	20
β-strand	149	1	19
β-strand	154-157	4	22
α-helix	158-160	3
β-strand	162	1	22
β-strand	166-168	3	20
α-helix	169-171	3
β-strand	172-173	2	20
α-helix	174	1
β-strand	179-188	10	20
β-strand	198-203	6	22
α-helix	204-206	3
β-strand	208-213	6	22

Chain LLL: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-7	3	23
β-strand	10-14	5	24
β-strand	19-24	6	23
β-strand	33-38	6	24
β-strand	44-49	6	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	84-90	7	24
α-helix	96	1
β-strand	97-98	2	24
β-strand	102-107	6	24
β-strand	111	1	25
α-helix	112-113	2
β-strand	114-118	5	26
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	26
β-strand	140	1	25
β-strand	145-150	6	27
β-strand	153-155	3	27
β-strand	159-163	5	26
α-helix	164-167	4
β-strand	173-182	10	26
α-helix	183-188	6
β-strand	192-197	6	27
β-strand	205-208	4	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DutaFab mat VH chain	AAA, HHH	protein	220	Homo sapiens
DutaFab mat VL chain	BBB, LLL	protein	214	Homo sapiens
Platelet-derived growth factor subunit B	CCC, DDD	protein	109	Homo sapiens	P01127 (AlphaFold model)

Sequence of entity 1 (AAA, HHH), FASTA

>6T9E_1 DutaFab mat VH chain (chains AAA, HHH)
DLQLVESGGGLVKPGGSLRLSCAADGWWFGYTDMSWVRQAPGKGLEWVGSISYKGGSTYY
NTKFIGRFTISRDDDTNTLYLQMNSLRAEDTAVYYCARDDGYFDTWGQGTLVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTKTYICNVNHKPSNTKVDKKVEPKSCT

Sequence of entity 2 (BBB, LLL), FASTA

>6T9E_2 DutaFab mat VL chain (chains BBB, LLL)
AIQMTQSPSSLSASVGDRVTITCHGSYWLSNYLAWYQQKPGKAPKLLIYDGKEREHGVPS
RFSGSGSHEDYTLTISSLQPEDFATYYCQQYRYHPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (CCC, DDD), FASTA

>6T9E_3 Platelet-derived growth factor subunit B (chains CCC, DDD)
SLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQC
RPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAAARPVT

Primary citation

DutaFabs are engineered therapeutic Fab fragments that can bind two targets simultaneously. Beckmann, R., Jensen, K., Fenn, S. et al. Nat Commun (2021) 12:708-708. DOI 10.1038/s41467-021-20949-3 · PubMed

Other PDB entries of the same protein (UniProt P01127 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HQU 2.2 Å, Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer…
3MJG 2.3 Å, The structure of a platelet derived growth factor receptor complex
4HQX 2.3 Å, CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer…
4QCI 2.3 Å, PDGF-B blocking antibody bound to PDGF-BB
1PDG 3.0 Å, Crystal structure of human platelet-derived growth factor bb

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