3FO9: Aldolase antibody 33F12 Fab'

Crystal structure of aldolase antibody 33F12 Fab' in complex with hapten 1,3-diketone. Determined by X-ray diffraction at 1.9 Å resolution. Released 22 Dec 2009.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,028
Mol. weight: 96.58 kDa
Ligands: DIK
Released: 22 Dec 2009

Explore 3FO9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FO9 contains 36 α-helices and 91 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	27C-27E	3	14
β-strand	30-31	2	14
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-155	3	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-188	6
β-strand	191-197	7	17
α-helix	204	1
β-strand	205-210	6	17

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	33-40	8	19
β-strand	44-51	8	19
α-helix	52B-53	3
β-strand	57-59	3	19
β-strand	64	1	18
β-strand	67-72	6	18
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-96	9	19
β-strand	99-103	4	19
β-strand	107-111	5	19
α-helix	115-116	2
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
α-helix	125-127	3
β-strand	137-147	11	21
β-strand	148	1	20
β-strand	153-157	4	22
α-helix	162-164	3
β-strand	166	1	22
β-strand	171-173	3	21
α-helix	174-176	3
β-strand	177-178	2	21
β-strand	185-194	10	21
β-strand	206-212	6	22
α-helix	213-215	3
β-strand	217-222	6	22

Chain H: 10 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
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	99-103	4	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-179	3	10
β-strand	184-194	11	10
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain L: 8 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-27E	3	3
β-strand	30-31	2	3
β-strand	33-38	6	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
α-helix	96	1
β-strand	97-98	2	2
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	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	144-150	7	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	191-198	8	6
α-helix	204	1
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin IGG2A - light chain	A, L	protein	219	Mus musculus
Immunoglobulin IGG2A - heavy chain	B, H	protein	218	Mus musculus	P01865 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>3FO9_1 Immunoglobulin IGG2A - light chain (chains A, L)
ELVMTQTPLSLPVSLGDQASISCRSSQSLVHSYGNTFLNWYLQKSGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, H), FASTA

>3FO9_2 Immunoglobulin IGG2A - heavy chain (chains B, H)
EVKLEESGGGLVQPGGSMKLSCVVSGLTFSRFWMSWVRQSPEKGLEWVAEIRLKSDNYAT
HYAESVKGKFTISRDDSKSRLYLQMNSLRTEDTGIYYCKIYFYSFSYWGQGTLVTVSAAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Ligands and cofactors

ID	Name	Formula	Copies
DIK	5-{[4-(5-methyl-3-oxohex-4-en-1-yl)phenyl]amino}-5-oxopentanoic acid	C18 H23 N O4	2

Primary citation

Direct observation of an enamine intermediate in amine catalysis. Zhu, X., Tanaka, F., Lerner, R.A. et al. J Am Chem Soc (2009) 131:18206-18207. DOI 10.1021/ja907271a · PubMed

Other PDB entries of the same protein (UniProt P01865 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NCW 1.3 Å, Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid
1RUK 1.4 Å, Crystal structure (C) of native cationic cyclization antibody 4C6 fab at pH 4.6 with a…
1RUP 1.4 Å, Crystal structure (G) of native cationic cyclization antibody 4C6 fab at pH 8.5 with a…
1RUM 1.48 Å, Crystal structure (F) of H2O2-soaked cationic cyclization antibody 4C6 fab at pH 8.5…
1RUA 1.75 Å, Crystal structure (B) of u.v.-irradiated cationic cyclization antibody 4C6 fab at pH 4.6…
1NBY 1.8 Å, Crystal Structure of HyHEL-63 complexed with HEL mutant K96A
1FLR 1.85 Å, 4-4-20 FAB fragment
6UQC 1.87 Å, Mouse IgG2a Bispecific Fc
1RUL 1.88 Å, Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6…
1NDG 1.9 Å, Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme
2ADF 1.9 Å, Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody…
1E4W 1.95 Å, crossreactive binding of a circularized peptide to an anti-TGFalpha antibody Fab-fragment

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