4QCI: PDGF-B blocking antibody

PDGF-B blocking antibody bound to PDGF-BB. Determined by X-ray diffraction at 2.3 Å resolution. Released 11 Mar 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,086
Mol. weight: 117.42 kDa
Released: 11 Mar 2015

Explore 4QCI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QCI contains 35 α-helices and 105 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 A: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-12	4	2
α-helix	17	1
β-strand	18-23	6	1
α-helix	27-29	3
β-strand	30	1	3
β-strand	33-37	5	2
β-strand	44-47	4	2
β-strand	48	1	4
β-strand	52	1	4
α-helix	53-54	2
β-strand	61-66	6	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	83-88	6	2
β-strand	97	1	2
β-strand	101-105	5	2
α-helix	107-108	2
β-strand	109	1	5
α-helix	110-111	2
β-strand	112-116	5	6
α-helix	117-119	3
α-helix	120-123	4
β-strand	127-137	11	6
β-strand	138	1	5
β-strand	143-148	6	7
β-strand	151-153	3	7
β-strand	157-159	3	6
α-helix	160-162	3
β-strand	163-165	3	6
β-strand	168-178	11	6
α-helix	179-184	6
β-strand	188-194	7	7
β-strand	197-203	7	7

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	109-110	2	10
β-strand	114-116	3	10
β-strand	117-118	2	9
β-strand	124	1	11
α-helix	125-126	2
β-strand	127-131	5	12
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	158-161	4	13
α-helix	162-164	3
β-strand	166	1	13
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	176-177	2	12
β-strand	182-191	10	12
β-strand	201-206	6	13
α-helix	207-209	3
β-strand	211-216	6	13

Chain C: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-24	8	14
α-helix	27-30	4
β-strand	37-40	4	15
β-strand	43-50	8	14
β-strand	59-76	18	15
β-strand	83-100	18	15

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8	1
β-strand	9-10	2	15
α-helix	11	1
β-strand	13	1	14
β-strand	17-24	8	16
β-strand	37-40	4	3
β-strand	43-50	8	16
β-strand	59-76	18	3
β-strand	83-100	18	3

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	33-39	7	19
β-strand	45-51	7	19
β-strand	58-60	3	19
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	109-110	2	19
β-strand	114-116	3	19
β-strand	117-118	2	18
β-strand	124	1	20
α-helix	125-126	2
β-strand	127-131	5	21
β-strand	143-152	10	21
β-strand	153	1	20
β-strand	158-161	4	22
α-helix	162-164	3
β-strand	170-172	3	21
α-helix	173-175	3
β-strand	176-177	2	21
β-strand	182-190	9	21
β-strand	201-206	6	22
α-helix	207-209	3
β-strand	211-216	6	22

Chain L: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	23
β-strand	9-12	4	24
α-helix	17	1
β-strand	18-23	6	23
α-helix	27-29	3
β-strand	30	1	15
β-strand	33-37	5	24
β-strand	44-47	4	24
β-strand	48	1	25
β-strand	52	1	25
α-helix	53-54	2
β-strand	61-66	6	23
β-strand	69-74	6	23
α-helix	79-81	3
β-strand	83-88	6	24
β-strand	97	1	24
β-strand	101-105	5	24
α-helix	107-108	2
β-strand	109	1	26
α-helix	110-111	2
β-strand	112-116	5	27
α-helix	117-119	3
α-helix	120-123	4
β-strand	127-137	11	27
β-strand	138	1	26
β-strand	143-148	6	28
β-strand	151-153	3	28
β-strand	157-159	3	27
α-helix	160-162	3
β-strand	163-164	2	27
β-strand	169-178	10	27
α-helix	179-184	6
β-strand	188-194	7	28
β-strand	197-203	7	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-PDGF-BB antibody - Light Chain	A, L	protein	209	Homo sapiens
anti-PDGF-BB antibody - Heavy chain	B, H	protein	223	Homo sapiens
Platelet-derived growth factor subunit B	C, D	protein	110	Homo sapiens	P01127 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>4QCI_1 anti-PDGF-BB antibody -  Light Chain (chains A, L)
SYELTQPPSVSVAPGQTARISCSGDSLGSYFVHWYQQKPGQAPVLVIYDDSNRPSGIPER
FSGSNSGNTATLTISGTQAEDEADYYCSAFTHNSDVFGGGTKLTVLPKSTPTLTVFPPSS
EELKENKATLVCLISNFSPSGVTVAWKANGTPITQGVDTSNPTKEGNKFMASSFLHLTSD
QWRSHNSFTCQVTHEGDTVEKSLSPAECL

Sequence of entity 2 (B, H), FASTA

>4QCI_2 anti-PDGF-BB antibody - Heavy chain (chains B, H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSYISDDGSLKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARHPYWYGGQLDLWGQGTLVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG

Sequence of entity 3 (C, D), FASTA

>4QCI_3 Platelet-derived growth factor subunit B (chains C, D)
MSLGSLTIAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQ
CRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCETVAAARPVT

Primary citation

Characterization of Binding Mode of Action of a Blocking Anti-Platelet-Derived Growth Factor (PDGF)-B Monoclonal Antibody, MOR8457, Reveals Conformational Flexibility and Avidity Needed for PDGF-BB To Bind PDGF Receptor-beta. Kuai, J., Mosyak, L., Brooks, J. et al. Biochemistry (2015) 54:1918-1929. DOI 10.1021/bi5015425 · 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…
6T9E 2.99 Å, Crystal structure of a bispecific DutaFab in complex with human PDGF
1PDG 3.0 Å, Crystal structure of human platelet-derived growth factor bb

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