5IKC: N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN

X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB. Determined by X-ray diffraction at 2.06 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 2.06 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 8,308
Mol. weight: 113.49 kDa
Released: 18 May 2016

Explore 5IKC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IKC contains 34 α-helices and 93 β-strands across 6 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
α-helix	43-44	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	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
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	144-150	7	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-198	8	5
β-strand	201-210	10	5

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	44-51	8	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	105	1	2
β-strand	109-113	5	2
α-helix	116-118	3
β-strand	119	1	7
α-helix	120-121	2
β-strand	122-126	5	8
β-strand	134	1	9
β-strand	137-147	11	8
β-strand	148	1	7
β-strand	153-157	5	10
β-strand	165-173	9	8
β-strand	176-186	11	8
β-strand	196-201	6	10
α-helix	202-204	3
β-strand	206-211	6	10

Chain H: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-40	7	12
β-strand	44-52	9	12
β-strand	57-60	4	12
α-helix	62-64	3
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	105	1	12
β-strand	109-113	5	12
β-strand	119	1	13
α-helix	120-121	2
β-strand	122-126	5	9
β-strand	137-147	11	9
β-strand	148	1	13
β-strand	153-156	4	14
α-helix	162-164	3
β-strand	166-173	8	9
β-strand	176-186	11	9
β-strand	196-201	6	14
α-helix	202-204	3
β-strand	206-211	6	14

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	15
β-strand	10-13	4	16
β-strand	19-25	7	15
β-strand	33-38	6	16
β-strand	45-49	5	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62-67	6	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	85-90	6	16
α-helix	96	1
β-strand	97-98	2	16
β-strand	102-106	5	16
β-strand	111	1	17
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-155	3	19
β-strand	159-163	5	18
β-strand	173-182	10	18
α-helix	183-186	4
β-strand	191-197	7	19
β-strand	205-210	6	19

Chain M: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	53-59	7	20
β-strand	68-72	5	20
α-helix	80-91	12
β-strand	103-106	4	20
β-strand	112	1	20
α-helix	116-118	3
β-strand	124-128	5	20

Chain N: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	53-59	7	21
β-strand	68-72	5	21
α-helix	80-90	11
β-strand	103-106	4	21
β-strand	112	1	21
α-helix	116-118	3
β-strand	124-128	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MAb 6H10 light chain	A, L	protein	213	Mus musculus	A0A0U5BC76 (AlphaFold model)
Ighg protein	B, H	protein	215	Mus musculus	Q569X1 (AlphaFold model)
Neuronal migration protein doublecortin	M, N	protein	90	Homo sapiens	O43602 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>5IKC_1 MAb 6H10 light chain (chains A, L)
DIVMTQSQKLMSTSVGDRVSITCKASQIVDTAVAWYQQKPGQSPKPLIYLASNRHTGVPD
RFTGSGSGTDFTLTINNVQSDDLADYFCLQHWNYPLTFGAGTKLELKGADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 2 (B, H), FASTA

>5IKC_2 Ighg protein (chains B, H)
QVQLQQSGADLVRPGASVKLSCTASGFDIKDDYVHWVKQRPEQGLEWIGRIDPANGATKY
APKFQDKATLTADTSSNTAYLQLSSLTSEDTAVYYCGRSKYFDSWGQGTTLTVSSAKTTP
PSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMS
SSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS

Sequence of entity 3 (M, N), FASTA

>5IKC_3 Neuronal migration protein doublecortin (chains M, N)
AAKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRYIYTIDGS
RKIGSMDELEEGESYVCSSDNFFKKVEYTK

Primary citation

Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies. Burger, D., Stihle, M., Sharma, A. et al. J Biol Chem (2016) 291:16292-16306. DOI 10.1074/jbc.M116.726547 · PubMed

Other PDB entries of the same protein (UniProt A0A0U5BC76 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VLP 2.9 Å, PCSK9 complex with LDLR antagonist peptide and Fab7G7
6U3I 2.9 Å, Design of organo-peptides as bipartite PCSK9 antagonists
6U2F 2.94 Å, PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2
6VRH 3.3 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine…
6VRL 3.8 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with…
6VRK 4.1 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with…

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