3BKM: Anti-amyloid-beta Fab WO2

Structure of anti-amyloid-beta Fab WO2 (Form A, P212121). Determined by X-ray diffraction at 1.6 Å resolution. Released 15 Apr 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,900
Mol. weight: 52.36 kDa
Ligands: ZN
Released: 15 Apr 2008

Explore 3BKM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BKM contains 18 α-helices and 46 β-strands across 2 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
α-helix	16-17	2
β-strand	18-25	8	7
α-helix	29-32	4
β-strand	35-40	8	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	64-66	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-97	10	9
β-strand	100E-103	6	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	114-116	3
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
α-helix	128-130	3
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-171	3	11
β-strand	174-184	11	11
β-strand	194-199	6	12
α-helix	200-202	3
β-strand	204-209	6	12

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	27C	1	3
β-strand	31	1	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	110	1	4
α-helix	111-112	2
β-strand	113-117	5	5
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	5
β-strand	139	1	4
β-strand	144-149	6	6
β-strand	152-153	2	6
β-strand	158-162	5	5
α-helix	163-166	4
β-strand	172-181	10	5
α-helix	182-187	6
β-strand	190-196	7	6
β-strand	204-209	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WO2 IgG2a Fab fragment Light Chain Kappa	L	protein	252	Mus musculus	P01837 (AlphaFold model)
WO2 IgG2a Fab fragment Heavy Chain	H	protein	224	Mus musculus	P84751 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>3BKM_1 WO2 IgG2a Fab fragment Light Chain Kappa (chains L)
DQSPQAVSSGCLLKMKLPVRLLVLMFWIPGSSSDVLMTQTPLSLPVNLGEQASISCRSSQ
SIVHSNGHTYLEWYLQRPGQSPKLLIYQVSTRFSGVPDRFSGSGSGTDFTLRISRVEAED
LGVYYCFQASLVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPK
DINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTST
SPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>3BKM_2 WO2 IgG2a Fab fragment Heavy Chain (chains H)
VTLKESGPGLLKPSQTLSLTCSFSGFSIRTSKVGVSWIRQPSGKGLEWLAHIYWDDDKRY
NPSLESRLTISKDTSRDMVFMKITSVDTADTATYYCARRGFYGRKYEVNHFDYWGQGTTL
TVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAV
LQSDLYTLSSSVTVTSSTWPSESITCNVAHPASSTKVDKKIVPR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope. Miles, L.A., Wun, K.S., Crespi, G.A. et al. J Mol Biol (2008) 377:181-192. DOI 10.1016/j.jmb.2007.12.036 · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…
2R23 1.65 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues

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