5IP4: C-terminal domain of human doublecortin

X-ray structure of the C-terminal domain of human doublecortin. Determined by X-ray diffraction at 1.81 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Lama glama, Homo sapiens
Chains: 4
Atoms: 3,373
Mol. weight: 47.55 kDa
Released: 18 May 2016

Explore 5IP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IP4 contains 14 α-helices and 33 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	12-14	3	2
β-strand	20-26	7	1
β-strand	36-41	6	2
α-helix	46-47	2
β-strand	48-53	6	2
β-strand	58-60	3	2
β-strand	65	1	1
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	3
β-strand	12-15	4	4
β-strand	20-26	7	3
β-strand	36-41	6	4
β-strand	47-53	7	4
β-strand	58-60	3	4
α-helix	62-64	3
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-98	7	4
β-strand	102-103	2	4
β-strand	107-112	6	4

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	260	1
β-strand	261-268	8	5
β-strand	275-280	6	5
α-helix	288-298	11
β-strand	309-311	3	5
β-strand	316-317	2	5
α-helix	320-323	4
β-strand	329-333	5	5

Chain E: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	260	1
β-strand	261-267	7	6
β-strand	275-280	6	6
α-helix	288-299	12
β-strand	308-311	4	6
α-helix	315	1
β-strand	316	1	6
α-helix	317	1
α-helix	320-322	3
β-strand	329-333	5	6
α-helix	335-337	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
XA4551 nanobody against C-dcx	A, B	protein	121	Lama glama
Neuronal migration protein doublecortin	D, E	protein	91	Homo sapiens	O43602 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IP4_1 XA4551 NANOBODY AGAINST C-DCX (chains A, B)
QVQLQESGGGLVQAGGSLRLSCTASVNIIGGNHWAWYRQAPGQQRDLVASLSRYNANYAD
SVKGRFTISRDNAKNAAYLQMNSLKPEDTAIYFCALENYYWGQGTQVTVSSHHHHHHEPE
A

Sequence of entity 2 (D, E), FASTA

>5IP4_2 Neuronal migration protein doublecortin (chains D, E)
ARENKDFVRPKLVTIIRSGVKPRKAVRVLLNKKTAHSFEQVLTDITEAIKLETGVVKKLY
TLDGKQVTCLHDFFGDDDVFIACGPEKFRYA

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 O43602 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IO9 1.3 Å, X-ray structure of the N-terminal domain of human doublecortin
5IKC 2.06 Å, X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB
2BQQ 2.2 Å, X-ray Structure of the N-terminal Domain of Human Doublecortin
6FNZ 2.23 Å, Crystal Structure of domain-swapped C-terminal domain of human doublecortin
5IOI 2.4 Å, X-ray structure of the N-terminal domain of human doublecortin
5IN7 2.48 Å, X-ray structure of the N-terminal domain of human doublecortin
6REV 3.8 Å, Cryo-EM structure of the N-terminal DC repeat (NDC) of human doublecortin (DCX) bound to…
6RF8 3.8 Å, Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence)…
6RFD 3.9 Å, Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence)…
6RF2 4.2 Å, Cryo-EM structure of the C-terminal DC repeat (CDC) of human doublecortin (DCX) bound to…
2XRP 8.2 Å, Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF and 3HKE) Docked into…
4ATU 8.3 Å, Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) docked into an 8A cryo-EM…

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