6KE5: CavAb

Structure of CavAb in complex with Diltiazem and Amlodipine. Determined by X-ray diffraction at 2.8 Å resolution. Released 23 Oct 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Arcobacter butzleri RM4018
Chains: 4
Atoms: 7,576
Mol. weight: 135.04 kDa
Ligands: 6UB, D6C, G3P, CA
Released: 23 Oct 2019

Explore 6KE5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KE5 contains 69 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: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	1004-1007	4
α-helix	1014-1032	19
α-helix	1037-1040	4
α-helix	1042-1064	23
α-helix	1075-1087	13
α-helix	1101-1107	7
α-helix	1108-1111	4
α-helix	1115-1123	9
α-helix	1124-1126	3
α-helix	1131-1151	21
α-helix	1157-1160	4
α-helix	1163-1175	13
α-helix	1179	1
α-helix	1180-1184	5
α-helix	1185-1190	6
α-helix	1199-1217	19

Chain B: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	1003-1009	7
α-helix	1013-1033	21
α-helix	1035-1038	4
α-helix	1042-1067	26
α-helix	1068-1073	6
α-helix	1075-1086	12
α-helix	1096-1101	6
α-helix	1102-1105	4
α-helix	1107-1112	6
α-helix	1116-1124	9
α-helix	1127-1151	25
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1179	1
α-helix	1180-1184	5
α-helix	1185-1188	4
α-helix	1192-1194	3
α-helix	1195-1210	16

Chain C: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	1006-1009	4
α-helix	1012-1030	19
α-helix	1037-1040	4
α-helix	1042-1044	3
α-helix	1048-1066	19
α-helix	1071-1073	3
α-helix	1075-1087	13
α-helix	1102-1109	8
α-helix	1114-1123	10
α-helix	1127-1138	12
α-helix	1140-1149	10
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1180-1184	5
α-helix	1185-1187	3
α-helix	1194-1214	21

Chain D: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	1002-1008	7
α-helix	1012-1014	3
α-helix	1015-1019	5
α-helix	1020-1026	7
α-helix	1028-1031	4
α-helix	1036-1041	6
α-helix	1043-1066	24
α-helix	1075-1085	11
α-helix	1101-1107	7
α-helix	1108-1111	4
α-helix	1114-1124	11
α-helix	1134-1152	19
α-helix	1163-1174	12
α-helix	1180-1184	5
α-helix	1185-1190	6
α-helix	1192-1194	3
α-helix	1195-1210	16
α-helix	1214-1221	8
α-helix	1224-1227	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ion transport protein	A, B, C, D	protein	284	Arcobacter butzleri RM4018	A8EVM5 (AlphaFold model)

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

>6KE5_1 Ion transport protein (chains A, B, C, D)
DYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGV
YTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRV
LRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTL
GESFYTLFQVMTLDDWSNGIVRPLMEVYPYAYVFFIPFIFVVTFVMINLVVAIIVDAMAI
LNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Ligands and cofactors

ID	Name	Formula	Copies
6UB	amlodipine	C20 H25 Cl N2 O5	1
D6C	[(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2…	C22 H26 N2 O4 S	1
G3P	Sn-glycerol-3-phosphate	C3 H9 O6 P	5
CA	Calcium ion	Ca	3
LPC	[1-myristoyl-glycerol-3-yl]phosphonylcholine	C22 H47 N O7 P	3

Primary citation

Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+Channel. Tang, L., Gamal El-Din, T.M., Lenaeus, M.J. et al. Mol Pharmacol (2019) 96:485-492. DOI 10.1124/mol.119.117531 · 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)
5KLB 2.7 Å, Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A)
6C1K 2.7 Å, HypoPP mutant with ligand1

Browse structure collections

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