5VZX: Crenezumab Fab

Crystal structure of crenezumab Fab. Determined by X-ray diffraction at 2.5 Å resolution. Released 9 Aug 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,755
Mol. weight: 96.05 kDa
Released: 9 Aug 2017

Explore 5VZX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VZX contains 30 α-helices and 90 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 E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	46-51	6	13
β-strand	57-58	2	13
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-93	6	13
β-strand	103	1	13
β-strand	107-111	5	13
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-124	5	15
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	16
α-helix	155-157	3
β-strand	159	1	16
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-185	10	15
α-helix	186-191	6
β-strand	195-200	6	16
α-helix	201-203	3
β-strand	205-210	6	16

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	57-58	2	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-93	6	2
β-strand	103	1	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-189	4
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain I: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	27C	1	19
β-strand	31	1	19
β-strand	33-38	6	18
β-strand	44-49	6	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-187	5
β-strand	191-197	7	22
β-strand	205-210	6	22

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	27C	1	8
β-strand	31	1	8
β-strand	33-38	6	7
β-strand	44-49	6	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Crenezumab Fab heavy chain	E, H	protein	220	Homo sapiens	P0DOX5 (AlphaFold model)
Crenezumab Fab light chain	I, L	protein	219	Homo sapiens	Q0KKI6 (AlphaFold model)

Sequence of entity 1 (E, H), FASTA

>5VZX_1 Crenezumab Fab heavy chain (chains E, H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYGMSWVRQAPGKGLELVASINSNGGSTYY
PDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCASGDYWGQGTTVTVSSASTKGPSV
FPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV
VTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (I, L), FASTA

>5VZX_2 Crenezumab Fab light chain (chains I, L)
DIVMTQSPLSLPVTPGEPASISCRSSQSLVYSNGDTYLHWYLQKPGQSPQLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCSQSTHVPWTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Structure of Crenezumab Complex with Abeta Shows Loss of beta-Hairpin. Ultsch, M., Li, B., Maurer, T. et al. Sci Rep (2016) 6:39374. DOI 10.1038/srep39374 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…

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