1PZ5: Light chain of Fab

Structural basis of peptide-carbohydrate mimicry in an antibody combining site. Determined by X-ray diffraction at 1.8 Å resolution. Released 18 Nov 2003.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,902
Mol. weight: 48.26 kDa
Released: 18 Nov 2003

Explore 1PZ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PZ5 contains 18 α-helices and 45 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 A: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C	1	3
β-strand	31	1	3
β-strand	33-38	6	2
α-helix	43-44	2
β-strand	45-49	5	2
β-strand	53-54	2	2
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	97-98	2	2
β-strand	99	1	1
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
α-helix	204	1
β-strand	205-210	6	6

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	2
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-40	8	2
β-strand	44-51	8	2
α-helix	52B-53	3
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	100A-103	4	2
β-strand	107-111	5	2
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	136-145	10	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-171	3	9
β-strand	174-183	10	9
α-helix	185-187	3
β-strand	194-199	6	10
α-helix	200-202	3
β-strand	204-209	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of Fab (SYA/J6)	A	protein	215	Mus musculus	A2NHM3 (AlphaFold model)
Heavy chain of Fab (SYA/J6)	B	protein	220	Mus musculus	P01801 (AlphaFold model)
Octapeptide (MDWNMHAA)	C	protein	8

Sequence of entity 1 (A), FASTA

>1PZ5_1 Light chain of Fab (SYA/J6) (chains A)
DVVLTQTPLSLPVRLGDQASISCRSSQSLLHSDGNTYLHWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQTTHVPTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (B), FASTA

>1PZ5_2 Heavy chain of Fab (SYA/J6) (chains B)
EVKVEESGGGLVQPGGSMKLSCVASGFTFSNYWMEWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGGAVGAMDYWGQGTSVTVSS
ATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSG
FYSLSSLVTVPSSTWPSQTVICNVAHPASKVDLIKEISGP

Sequence of entity 3 (C), FASTA

>1PZ5_3 Octapeptide (MDWNMHAA) (chains C)
MDWNMHAA

Primary citation

Structural basis of peptide-carbohydrate mimicry in an antibody combining site. Vyas, N.K., Vyas, M.N., Chervenak, M.C. et al. Proc Natl Acad Sci U S A (2003) 100:15023-15028. DOI 10.1073/pnas.2431286100 · PubMed

Other PDB entries of the same protein (UniProt A2NHM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PXR 1.56 Å, Anti-TAU BIIB092 FAB with TAU peptide
4TPR 1.6 Å, Structure of Tau5 antibody Fab fragment
4TQE 1.6 Å, Structure of tau peptide in complex with Tau5 antibody Fab fragment
3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2IPU 1.65 Å, PFA1 Fab fragment complexed with Abeta 1-8 peptide
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2DQU 1.7 Å, Crystal form II: high resolution crystal structure of the complex of the hydrolytic…
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
1ZEA 1.78 Å, Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…
1T2Q 1.83 Å, The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen

Browse structure collections

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