1M7D: PDB entry 1M7D

Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide. Determined by X-ray diffraction at 2.3 Å resolution. Released 22 Jul 2003.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,478
Mol. weight: 47.78 kDa
Released: 22 Jul 2003

Explore 1M7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1M7D contains 14 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: 7 helices, 23 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
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
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
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
β-strand	205-210	6	6

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-40	8	8
β-strand	44-51	8	8
α-helix	52B-53	3
β-strand	57-59	3	8
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100A-103	4	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
β-strand	120-124	5	10
β-strand	136-145	10	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-171	3	10
β-strand	174-183	10	10
β-strand	195-199	5	11
α-helix	200-202	3
β-strand	204-208	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
light chain of the monoclonal antibody Fab SYA/J6	A	protein	215	Mus musculus	A2NHM3 (AlphaFold model)
heavy chain of the monoclonal antibody Fab SYA/J6	B	protein	220	Mus musculus	P01801 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1M7D_1 light chain of the monoclonal antibody Fab SYA/J6 (chains A)
DVVLTQTPLSLPVRLGDQASISCRSSQSLLHSDGNTYLHWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQTTHVPTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (B), FASTA

>1M7D_2 heavy chain of the monoclonal antibody Fab SYA/J6 (chains B)
EVKVEESGGGLVQPGGSMKLSCVASGFTFSNYWMEWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGGAVGAMDYWGQGTSVTVSS
ATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSG
FYSLSSLVTVPSSTWPSQTVICNVAHPASKVDLIKEPSGP

Primary citation

Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics. Vyas, N.K., Vyas, M.N., Chervenak, M.C. et al. Biochemistry (2002) 41:13575-13586. DOI 10.1021/bi0261387 · 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
1PZ5 1.8 Å, Structural basis of peptide-carbohydrate mimicry in an antibody combining site
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…

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