1GPO: Antibody M41

Crystal structure of the rationally designed antibody M41 as a FAB fragment. Determined by X-ray diffraction at 1.95 Å resolution. Released 1 Apr 1998.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,281
Mol. weight: 96.9 kDa
Released: 1 Apr 1998

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

Secondary structure: helices and β-sheets

1GPO contains 29 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 H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-97	7	9
β-strand	103	1	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
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 I: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	21
β-strand	45-51	7	21
β-strand	57-59	3	21
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	87-89	3
β-strand	91-97	7	21
β-strand	103	1	21
β-strand	107-109	3	21
β-strand	110-111	2	20
α-helix	115-116	2
β-strand	117	1	22
β-strand	120-124	5	23
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	151-154	4	24
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-171	3	23
β-strand	174-184	11	23
β-strand	193-199	7	24
α-helix	200-202	3
β-strand	204-210	7	24

Chain L: 9 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	30	1	3
β-strand	36	1	3
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	90-95	6	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	116	1	4
α-helix	117-118	2
β-strand	119-123	5	5
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	5
β-strand	145	1	4
β-strand	150-155	6	6
β-strand	158-160	3	6
β-strand	164-168	5	5
α-helix	169-172	4
β-strand	178-187	10	5
α-helix	188-191	4
β-strand	196-202	7	6
α-helix	209	1
β-strand	210-215	6	6

Chain M: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	30	1	15
β-strand	36	1	15
β-strand	38-43	6	14
β-strand	50-54	5	14
β-strand	58-59	2	14
β-strand	67-72	6	13
β-strand	75-80	6	13
α-helix	85-87	3
β-strand	90-95	6	14
α-helix	101	1
β-strand	102-103	2	14
β-strand	107-111	5	14
β-strand	116	1	16
β-strand	119-123	5	17
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	17
β-strand	145	1	16
β-strand	150-155	6	18
β-strand	164-168	5	17
α-helix	169-172	4
β-strand	178-187	10	17
α-helix	188-191	4
β-strand	196-202	7	18
β-strand	210-215	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody M41	L, M	protein	219	Mus musculus	P01837 (AlphaFold model)
Antibody M41	H, I	protein	221	Mus musculus	P01868 (AlphaFold model)

Sequence of entity 1 (L, M), FASTA

>1GPO_1 ANTIBODY M41 (chains L, M)
DIELTQSPATLSVTPGNSVSISCRASQSLVNEDGNTYLFWYQQKSHESPRLLIKYASQSI
SGIPSRFSGSGSGTDFTLSINSVETEDLAVYFCQQITDWPFTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H, I), FASTA

>1GPO_2 ANTIBODY M41 (chains H, I)
EVKLQESGPSLVKPSQTLSLTCSVTGDSITSDFWSWIRQFPGNRLEYMGFVQYSGETAYN
PSLKSRISITRDTSKNQYYLDLNSVTTEDTAVYYCANWHGDYWGQGTTVTVSSAKTTPPS
VYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCHHHHHH

Primary citation

The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment. Schiweck, W., Skerra, A. J Mol Biol (1997) 268:934-951. DOI 10.1006/jmbi.1997.1006 · 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
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…

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