2GK0: Catalytic elimination antibody 13G5 light chain

Structure of Catalytic Elimination Antibody 13G5 from a twinned crystal in space group C2. Determined by X-ray diffraction at 2.45 Å resolution. Released 6 Feb 2007.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,692
Mol. weight: 94.84 kDa
Released: 6 Feb 2007

Explore 2GK0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2GK0 contains 21 α-helices and 100 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 A: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10	1	15
β-strand	13-14	2	16
β-strand	19-25	7	14
β-strand	33-38	6	15
α-helix	42-44	3
β-strand	45-46	2	15
β-strand	48	1	17
β-strand	54	1	17
α-helix	55	1
β-strand	62-64	3	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-90	7	15
α-helix	96	1
β-strand	97-98	2	15
β-strand	102-104	3	15
β-strand	106-107	2	16
β-strand	111	1	18
β-strand	114-118	5	19
α-helix	122-125	4
β-strand	130-139	10	19
β-strand	140	1	18
β-strand	145-149	5	20
β-strand	154-155	2	20
β-strand	159-163	5	19
α-helix	165-167	3
β-strand	173-181	9	19
α-helix	183-186	4
β-strand	192	1	21
β-strand	193-197	5	20
β-strand	198	1	22
β-strand	201	1	22
α-helix	204-205	2
β-strand	209	1	21

Chain B: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	11-12	2	24
β-strand	21-25	5	23
β-strand	34-39	6	25
β-strand	46-51	6	25
β-strand	57-59	3	25
α-helix	61-63	3
β-strand	72	1	23
β-strand	77-78	2	23
β-strand	88-94	7	25
β-strand	103	1	25
β-strand	107-109	3	25
β-strand	110-111	2	24
β-strand	117	1	26
β-strand	120	1	27
β-strand	123-124	2	27
β-strand	137	1	28
β-strand	140-147	8	27
β-strand	148	1	26
β-strand	153	1	29
β-strand	157	1	29
α-helix	162-164	3
β-strand	171-174	4	27
β-strand	179	1	30
β-strand	184	1	30
β-strand	185-191	7	27
β-strand	194	1	28
α-helix	195-198	3
β-strand	206-211	5	29
β-strand	218-222	5	29

Chain H: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	21-25	5	7
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	69	1	10
β-strand	72	1	7
α-helix	73-75	3
β-strand	77	1	7
β-strand	80	1	10
β-strand	88-95	8	9
β-strand	100E-103	4	9
β-strand	107-109	3	9
β-strand	110-111	2	8
β-strand	117	1	11
α-helix	118-119	2
β-strand	120	1	12
β-strand	123-124	2	12
β-strand	137-147	11	12
β-strand	148	1	11
β-strand	153-157	4	13
α-helix	162-164	3
β-strand	171-179	9	12
β-strand	184-194	11	12
β-strand	206-211	5	13
β-strand	218-222	5	13

Chain L: 6 helices, 22 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	33-38	6	2
α-helix	43	1
β-strand	44-48	5	2
β-strand	54	1	2
α-helix	55	1
β-strand	62-66	5	1
β-strand	70-75	6	1
β-strand	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-149	6	5
β-strand	154-155	2	5
β-strand	160-163	4	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	192	1	6
β-strand	193-198	6	5
β-strand	209	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Catalytic elimination antibody 13G5 light chain	A, L	protein	217	Mus musculus	Q65ZC0 (AlphaFold model)
Catalytic elimination antibody 13G5 heavy chain	B, H	protein	221	Mus musculus	P01867 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>2GK0_1 Catalytic elimination antibody 13G5 light chain (chains A, L)
ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKINRVEAEDLGVYYCFQGSHLPPTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 2 (B, H), FASTA

>2GK0_2 Catalytic elimination antibody 13G5 heavy chain (chains B, H)
QVQLKESGPGLVAPSQSLSITCTVSGFSLTNYGVDWVRQPPGKGLEWVGVIWSGGSTNYN
SALMSRLSISKDNSKSQVFLKMNSLQTDDTAVYYCAKHWGGYYIPYGMDHWGQGTTVTVS
SAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPEPVTVTWNSGSLSSSVHTFPALLQS
GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPR

Primary citation

Bifunctional Catalysis of Proton Transfer at an Antibody Active Site. Muller, R., Debler, E.W., Steinmann, M. et al. J Am Chem Soc (2007) 129:460-461. DOI 10.1021/ja066578b · PubMed

Other PDB entries of the same protein (UniProt Q65ZC0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2G60 1.85 Å, Structure of anti-FLAG M2 Fab domain
1LO2 2.0 Å, Retro-Diels-Alderase Catalytic Antibody
1L7T 2.1 Å, Crystal Structure Analysis of the anti-testosterone Fab fragment
1LO3 2.3 Å, Retro-Diels-Alderase Catalytic Antibody: Product Analogue
1T66 2.3 Å, The structure of FAB with intermediate affinity for fluorescein.
1LO4 2.4 Å, Retro-Diels-Alderase Catalytic antibody 9D9
1I9J 2.6 Å, Testosterone complex structure of the recombinant monoclonal wild type anti-testosterone…
2GJZ 2.65 Å, Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)
1I9I 2.72 Å, Native crystal structure of the recombinant monoclonal wild type anti-testosterone FAB…

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