5VVM: Human CDH23 EC21-23

Crystal structure of human CDH23 EC21-23. Determined by X-ray diffraction at 3.54 Å resolution. Released 23 May 2018.

Method: X-ray diffraction
Resolution: 3.54 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,670
Mol. weight: 76.27 kDa
Ligands: CA
Released: 23 May 2018

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

Secondary structure: helices and β-sheets

5VVM contains 14 α-helices and 52 β-strands across 2 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: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2157-2161	5	1
α-helix	2164-2165	2
β-strand	2169-2172	4	2
β-strand	2184-2194	11	1
β-strand	2200-2201	2	1
β-strand	2208-2210	3	2
β-strand	2216-2219	4	2
β-strand	2230-2239	10	1
β-strand	2250-2261	12	1
β-strand	2269-2270	2	3
β-strand	2278-2283	6	4
α-helix	2286-2287	2
β-strand	2291-2294	4	5
β-strand	2297-2298	2	3
α-helix	2303-2306	4
β-strand	2308-2313	6	4
β-strand	2321-2323	3	5
β-strand	2330-2333	4	5
β-strand	2344-2353	10	4
α-helix	2358-2359	2
β-strand	2360-2370	11	4
α-helix	2371	1
β-strand	2377-2379	3	6
β-strand	2383	1	7
β-strand	2403-2405	3	6
β-strand	2415-2417	3	8
β-strand	2453-2455	3	8
α-helix	2462-2464	3
β-strand	2467-2469	3	8
β-strand	2471	1	7

Chain B: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2151	1	9
β-strand	2155-2161	7	10
α-helix	2164-2165	2
β-strand	2169-2172	4	11
β-strand	2175	1	9
β-strand	2184-2194	11	10
β-strand	2200-2201	2	10
β-strand	2208-2210	3	11
β-strand	2216-2219	4	11
β-strand	2230-2239	10	10
β-strand	2249	1	10
α-helix	2253	1
β-strand	2254-2261	8	10
β-strand	2269-2271	3	12
β-strand	2278-2283	6	13
α-helix	2286-2287	2
β-strand	2291-2294	4	14
β-strand	2296-2298	3	12
α-helix	2303-2306	4
β-strand	2308-2316	9	13
β-strand	2321-2323	3	14
β-strand	2330-2333	4	14
β-strand	2344-2353	10	13
α-helix	2358-2359	2
β-strand	2360-2370	11	13
α-helix	2371	1
β-strand	2377-2379	3	15
β-strand	2383-2384	2	16
α-helix	2392-2393	2
β-strand	2403-2405	3	15
β-strand	2415-2418	4	16
β-strand	2425-2427	3	17
β-strand	2434-2436	3	17
β-strand	2450-2455	6	16
α-helix	2462-2464	3
β-strand	2467-2472	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cadherin-23	A, B	protein	346	Homo sapiens	Q9H251 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VVM_1 Cadherin-23 (chains A, B)
MDSRPEFLNPIQTVSVLESAEPGTVIANITAIDHDLNPKLEYHIVGIVAKDDTDRLVPNQ
EDAFAVNINTGSVMVKSPMNRELVATYEVTLSVIDNASDLPERSVSVPNAKLTVNVLDVN
DNTPQFKPFGITYYMERILEGATPGTTLIAVAAVDPDKGLNGLVTYTLLDLVPPGYVQLE
DSSAGKVIANRTVDYEEVHWLNFTVRASDNGSPPRAAEIPVYLEIVDINDNNPIFDQPSY
QEAVFEDVPVGTIILTVTATDADSGNFALIEYSLGDGESKFAINPTTGDIYVLSSLDREK
KDHYILTALAKDNPGDVASNRRENSVQVVIQVLDVNDCLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12

Primary citation

Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Jaiganesh, A., De-la-Torre, P., Patel, A.A. et al. Structure (2018) 26:1210. DOI 10.1016/j.str.2018.06.003 · PubMed

Other PDB entries of the same protein (UniProt Q9H251 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WJ8 1.86 Å, Crystal Structure of Human Cadherin-23 EC13-14
5TFM 2.92 Å, Crystal Structure of Human Cadherin-23 EC6-8
2KBR Solution structure of harmonin N terminal domain in complex with a internal peptide of…
2KBS Solution structure of harmonin PDZ2 in complex with the carboxyl tail peptide of…
2LSR Solution structure of harmonin N terminal domain in complex with a exon68 encoded…

Browse structure collections

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