5KLB: Ion transport protein

Name: PDB 5KLB: Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A)
Published: 2016-08-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transport protein

Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A). Determined by X-ray diffraction at 2.7 Å resolution. Released 31 Aug 2016.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Arcobacter butzleri (strain RM4018)
Chains: 4
Atoms: 9,684
Mol. weight: 149.82 kDa
Ligands: CPS, CA, MC3
Released: 31 Aug 2016

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

Secondary structure: helices and β-sheets

5KLB contains 67 α-helices and 0 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: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	1002-1009	8
α-helix	1012-1031	20
α-helix	1037-1040	4
α-helix	1042-1067	26
α-helix	1068-1071	4
α-helix	1075-1086	12
α-helix	1098-1101	4
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1114-1124	11
α-helix	1127-1152	26
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1180-1184	5
α-helix	1185-1190	6
α-helix	1195-1245	51
α-helix	1252-1259	8

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	1002-1009	8
α-helix	1012-1031	20
α-helix	1035-1067	33
α-helix	1068-1073	6
α-helix	1075-1086	12
α-helix	1097-1101	5
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1114-1152	39
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1180-1184	5
α-helix	1185-1190	6
α-helix	1195-1239	45
α-helix	1245-1252	8

Chain C: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	1002-1009	8
α-helix	1012-1031	20
α-helix	1035-1039	5
α-helix	1043-1067	25
α-helix	1068-1073	6
α-helix	1075-1086	12
α-helix	1096-1101	6
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1114-1125	12
α-helix	1127-1152	26
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1180-1184	5
α-helix	1185-1190	6
α-helix	1195-1236	42
α-helix	1240-1244	5
α-helix	1252-1255	4
α-helix	1257-1260	4

Chain D: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	1002-1009	8
α-helix	1012-1031	20
α-helix	1035-1067	33
α-helix	1068-1073	6
α-helix	1075-1086	12
α-helix	1098-1101	4
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1114-1125	12
α-helix	1128-1130	3
α-helix	1131-1152	22
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1180-1184	5
α-helix	1185-1190	6
α-helix	1194-1262	69

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ion transport protein	A, B, C, D	protein	285	Arcobacter butzleri (strain RM4018)	A8EVM5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5KLB_1 Ion transport protein (chains A, B, C, D)
MDYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFG
VYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLR
VLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGT
LGESFYTLFQVMTLDDWSNGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMA
ILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Ligands and cofactors

ID	Name	Formula	Copies
CPS	3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate	C32 H58 N2 O7 S	6
CA	Calcium ion	Ca	3
MC3	1,2-dimyristoyl-rac-glycero-3-phosphocholine	C36 H72 N O8 P	20

Primary citation

Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs. Tang, L., El-Din, T.M., Swanson, T.M. et al. Nature (2016) 537:117-121. DOI 10.1038/nature19102 · PubMed

Other PDB entries of the same protein (UniProt A8EVM5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MWD 2.33 Å, NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206S
6MWA 2.4 Å, NavAb Voltage-gated Sodium Channel, residues 1-239
9UC1 2.5 Å, Crystal structure of voltage-gated sodium channel NavAb N49K/S178T mutant
6MWG 2.5 Å, NavAb Voltage-gated Sodium Channel, residues 1-239, with mutation T206V
6C1M 2.52 Å, NavAb NormoPP mutant
8DIV 2.54 Å, Crystal structure of NavAb I22V as a basis for the human Nav1.7 Inherited…
6MWB 2.6 Å, NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206A
8VGL 2.6 Å, CryoEM structure of Nav1.7 in complex with wild type Fab 7A9
8VGM 2.6 Å, CryoEM structure of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS
3RVY 2.7 Å, Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.7 A)
6C1K 2.7 Å, HypoPP mutant with ligand1
8DJ0 2.7 Å, Crystal structure of NavAb L123T as a basis for the human Nav1.7 Inherited…

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