3CFK: PDB entry 3CFK

Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 Apr 2008.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Mus musculus, Homo sapiens
Chains: 16
Atoms: 27,118
Mol. weight: 387.02 kDa
Ligands: CD, B3P
Released: 15 Apr 2008

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

Secondary structure: helices and β-sheets

3CFK contains 154 α-helices and 352 β-strands across 16 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.

Chains A, E and J: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	11
β-strand	9-13	4	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	43-49	7	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-76	7	11
α-helix	80-82	3
β-strand	84-92	9	12
β-strand	95-98	4	12
β-strand	102-106	5	12
α-helix	107	1
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
α-helix	155	1
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-186	4
β-strand	191-197	7	15
β-strand	205-210	6	15

Chains B and P: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	45-51	7	17
β-strand	57-59	3	17
β-strand	67-72	6	16
α-helix	73-75	3
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-96	9	17
β-strand	100E-103	5	17
β-strand	107-111	5	17
α-helix	115-116	2
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	134	1	19
β-strand	137-147	11	19
β-strand	148	1	18
β-strand	153-157	4	20
α-helix	162-164	3
β-strand	166	1	20
β-strand	171-173	3	19
α-helix	174-176	3
β-strand	177-178	2	19
β-strand	185-194	10	19
α-helix	195-200	6
β-strand	207-212	6	20
α-helix	213-215	3
β-strand	217-222	6	20

Chain C: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	21
β-strand	9-13	4	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	43-49	7	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-76	7	21
α-helix	80-82	3
β-strand	84-91	8	22
β-strand	96-98	3	22
β-strand	102-106	5	22
α-helix	107	1
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-154	2	25
α-helix	155	1
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-186	4
β-strand	191-197	7	25
β-strand	205-210	6	25

Chain D: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	33-39	7	27
β-strand	45-51	7	27
β-strand	57-59	3	27
α-helix	61-66	6
β-strand	67-72	6	26
α-helix	73-75	3
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-98	11	27
α-helix	99-100A	3
β-strand	100C-103	7	27
β-strand	107-111	5	27
α-helix	115-116	2
β-strand	117	1	28
α-helix	118-119	2
β-strand	120-124	5	29
β-strand	134	1	29
β-strand	137-147	11	29
β-strand	148	1	28
β-strand	153-157	4	30
α-helix	162-164	3
β-strand	166	1	30
β-strand	171-173	3	29
α-helix	174-176	3
β-strand	177-178	2	29
β-strand	185-194	10	29
α-helix	195-200	6
β-strand	207-212	6	30
α-helix	213-215	3
β-strand	217-222	6	30

Chains F and I: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	36
β-strand	10-12	3	37
β-strand	18-25	8	36
α-helix	29-31	3
β-strand	33-39	7	37
β-strand	45-51	7	37
β-strand	57-59	3	37
β-strand	67-72	6	36
α-helix	73-75	3
β-strand	77-82	6	36
α-helix	84-86	3
β-strand	88-96	9	37
β-strand	100E-103	5	37
β-strand	107-111	5	37
α-helix	115-116	2
β-strand	117	1	38
α-helix	118-119	2
β-strand	120-124	5	39
β-strand	134	1	39
β-strand	137-147	11	39
β-strand	148	1	38
β-strand	153-157	4	40
β-strand	166	1	40
β-strand	171-173	3	39
α-helix	174-176	3
β-strand	177-178	2	39
β-strand	185-194	10	39
α-helix	195-200	6
β-strand	207-212	6	40
α-helix	213-215	3
β-strand	217-222	6	40

Chains G, L and O: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	41
β-strand	9-13	4	42
β-strand	18-25	8	41
α-helix	29-31	3
β-strand	34-39	6	42
β-strand	43-49	7	42
β-strand	53-54	2	42
α-helix	55	1
β-strand	62-67	6	41
β-strand	70-76	7	41
α-helix	80-82	3
β-strand	84-92	9	42
β-strand	95-98	4	42
β-strand	102-106	5	42
α-helix	107	1
β-strand	111	1	43
α-helix	112-113	2
β-strand	114-118	5	44
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	44
β-strand	140	1	43
β-strand	145-150	6	45
β-strand	153-154	2	45
α-helix	155	1
β-strand	159-163	5	44
α-helix	164-167	4
β-strand	173-182	10	44
α-helix	183-186	4
β-strand	191-197	7	45
β-strand	205-210	6	45

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	45-51	7	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-98	11	7
β-strand	100C-103	7	7
β-strand	107-111	5	7
α-helix	115-116	2
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	134	1	9
β-strand	137-147	11	9
β-strand	148	1	8
β-strand	153-157	4	10
α-helix	162-164	3
β-strand	166	1	10
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	185-194	10	9
α-helix	195-200	6
β-strand	207-212	6	10
α-helix	213-215	3
β-strand	217-222	6	10

Chain K: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	56
β-strand	10-12	3	57
β-strand	18-25	8	56
α-helix	29-31	3
β-strand	33-39	7	57
β-strand	45-51	7	57
β-strand	57-59	3	57
α-helix	61-63	3
β-strand	67-72	6	56
α-helix	73-75	3
β-strand	77-82	6	56
α-helix	84-86	3
β-strand	88-98	11	57
α-helix	99-100A	3
β-strand	100C-103	7	57
β-strand	107-111	5	57
α-helix	115-116	2
β-strand	117	1	58
α-helix	118-119	2
β-strand	120-124	5	59
β-strand	134	1	59
β-strand	137-147	11	59
β-strand	148	1	58
β-strand	153-157	4	60
β-strand	166	1	60
β-strand	171-173	3	59
α-helix	174-176	3
β-strand	177-178	2	59
β-strand	185-194	10	59
α-helix	195-200	6
β-strand	207-212	6	60
α-helix	213-215	3
β-strand	217-222	6	60

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein	A, C, E, G, J, L, M, O	protein	216	Mus musculus, Homo sapiens	P01723 (AlphaFold model)
CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein	B, D, F, H, I, K, N, P	protein	227	Mus musculus, Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, J, L, M, O), FASTA

>3CFK_1 CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein (chains A, C, E, G, J, L, M, O)
ELVVTQESALTTSPGETVTLTCRSSSGAVTTSNYATWVQEKPDHLFTGLIGGTNKRAPGV
PARFSGSLIGDRAALTITGAQTEDEAIYFCALWNSNHLVFGGGTKLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D, F, H, I, K, N, P), FASTA

>3CFK_2 CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein (chains B, D, F, H, I, K, N, P)
EVKLLESGGGLAQPGGSLKLSCAASGFDFRRYWMTWVRQAPGKGLEWIGEINPDSRTINY
MPSLKDKFIISRDNAKNSLYLQLSRLRSEDSALYYCVRLDFDVYNHYYVLDYWGQGTSVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	23
B3P	2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-pr…	C11 H26 N2 O6	2

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

Primary citation

Conformational isomerism can limit antibody catalysis. Debler, E.W., Muller, R., Hilvert, D. et al. J Biol Chem (2008) 283:16554-16560. DOI 10.1074/jbc.M710256200 · PubMed

Other PDB entries of the same protein (UniProt P01723 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q0X 1.6 Å, Anti-morphine Antibody 9B1 Unliganded Form
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
1P4B 2.35 Å, Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide…
3CFJ 2.6 Å, Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal form
1P4I 2.8 Å, Crystal Structure of scFv against peptide GCN4

Browse structure collections

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