2W9D: Icsm 18-anti-prp therapeutic FAB heavy chain

Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A resolution. Determined by X-ray diffraction at 1.57 Å resolution. Released 3 Feb 2009.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: MUS MUSCULUS
Chains: 2
Atoms: 4,067
Mol. weight: 46.57 kDa
Ligands: CA
Released: 3 Feb 2009

Explore 2W9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W9D contains 17 α-helices and 43 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-24	7	1
α-helix	25	1
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-72	5	1
β-strand	79-83	5	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	103-106	4	2
β-strand	110-114	5	2
α-helix	117-119	3
β-strand	120	1	3
α-helix	121-122	2
β-strand	123-127	5	4
β-strand	137-147	11	4
β-strand	148	1	3
β-strand	153-156	4	5
α-helix	157-159	3
β-strand	161	1	5
β-strand	165-167	3	4
α-helix	168-170	3
β-strand	171-173	3	4
β-strand	176-186	11	4
β-strand	196-201	6	5
α-helix	202-204	3
β-strand	206-211	6	5

Chain L: 8 helices, 21 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	33-37	5	7
β-strand	44-48	5	7
β-strand	52-53	2	7
α-helix	54	1
β-strand	61-66	6	6
β-strand	69-74	6	6
α-helix	79-81	3
β-strand	83-89	7	7
α-helix	95	1
β-strand	96-97	2	7
β-strand	101-105	5	7
β-strand	110	1	8
α-helix	111-112	2
β-strand	113-117	5	9
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	9
β-strand	139	1	8
β-strand	144-149	6	10
β-strand	152-154	3	10
β-strand	158-162	5	9
α-helix	163-166	4
β-strand	172-181	10	9
α-helix	182-187	6
β-strand	190-196	7	10
β-strand	204-209	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Icsm 18-anti-prp therapeutic FAB heavy chain	H	protein	215	MUS MUSCULUS
Icsm 18-anti-prp therapeutic FAB light chain	L	protein	212	MUS MUSCULUS	P01837 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>2W9D_1 ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN (chains H)
EVQLQQSGPELVKPGSSVKISCKASRNTFTDYNLDWVKQSHGKTLEWIGNVYPNNGVTGY
NQKFRGKATLTVDKSSSTAYMELHSLTSEDSAVYYCALYYYDVSYWGQGTLVTVSSAKTT
PPSVYPLAPGSAAQTSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLS
SSVTVPSSTWPSQSVTCNVAHPASSTKVDKKITPR

Sequence of entity 2 (L), FASTA

>2W9D_2 ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN (chains L)
QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPAR
FSGSGSGTSYSLTISSMEAEDAATYFCHQWRSNPYTFGGGTKLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Crystal Structure of Human Prion Protein Bound to a Therapeutic Antibody. Antonyuk, S.V., Trevitt, C.R., Strange, R.W. et al. Proc Natl Acad Sci U S A (2009) 106:2554. DOI 10.1073/PNAS.0809170106 · 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
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
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
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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