1F3D: Catalytic antibody 4B2

Catalytic antibody 4B2 in complex with its amidinium hapten. Determined by X-ray diffraction at 1.87 Å resolution. Released 13 Sept 2000.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,035
Mol. weight: 95.5 kDa
Ligands: TPM
Released: 13 Sept 2000

Explore 1F3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1F3D contains 32 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-40	7	8
β-strand	44-51	8	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	64	1	7
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	102-103	2	8
β-strand	107-111	5	8
α-helix	122-124	3
β-strand	125	1	9
β-strand	128-132	5	10
β-strand	143-153	11	10
β-strand	154	1	9
β-strand	159-162	4	11
α-helix	163-165	3
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-179	3	10
β-strand	182-192	11	10
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain J: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	27C	1	14
β-strand	31	1	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	102-106	5	13
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
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	183-187	5
β-strand	191-197	7	17
α-helix	204	1
β-strand	205-210	6	17

Chain K: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-40	7	19
β-strand	44-51	8	19
β-strand	57-59	3	19
α-helix	61-63	3
β-strand	64	1	18
β-strand	67-72	6	18
α-helix	73-75	3
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-94	7	19
β-strand	103	1	19
β-strand	107-111	5	19
α-helix	122-124	3
β-strand	125	1	20
α-helix	126-127	2
β-strand	128-132	5	21
β-strand	143-153	11	21
β-strand	154	1	20
β-strand	159-162	4	22
α-helix	163-165	3
β-strand	171-173	3	21
α-helix	174-176	3
β-strand	177-179	3	21
β-strand	182-192	11	21
β-strand	202-207	6	22
α-helix	208-210	3
β-strand	212-217	6	22

Chain L: 7 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	27C	1	3
β-strand	31	1	3
β-strand	33-38	6	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
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	4
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Catalytic antibody 4B2	J, L	protein	219	Mus musculus	A2NHM3 (AlphaFold model)
Catalytic antibody 4B2	H, K	protein	217	Mus musculus

Sequence of entity 1 (J, L), FASTA

>1F3D_1 CATALYTIC ANTIBODY 4B2 (chains J, L)
DVLMTQTPLSLPVSLGDQVSISCRSSQSIFHSDGKTYLEWHLQKPGQSPKLLIYKVSKRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNAC

Sequence of entity 2 (H, K), FASTA

>1F3D_2 CATALYTIC ANTIBODY 4B2 (chains H, K)
EIQLQQSGPELVKPGASVKVSCKASGYSFIDYNIHWVKQSHGKSLEWIGYIVPYSGGTTF
NQKFKGKATLTVDKSSSTAFMHLNSLTFEDSAVYYCANDYDGVYWGQGTTLTVSSAKTTP
PSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLS
SSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Ligands and cofactors

ID	Name	Formula	Copies
TPM	2-(4-aminobenzylamino)-3,4,5,6-tetrahydropyridinium	C12 H18 N3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural evidence for a programmed general base in the active site of a catalytic antibody. Golinelli-Pimpaneau, B., Goncalves, O., Dintinger, T. et al. Proc Natl Acad Sci U S A (2000) 97:9892-9895. DOI 10.1073/pnas.97.18.9892 · 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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