5VKH: Closed conformation of KcsA Y82A-F103A mutant

Closed conformation of KcsA Y82A-F103A mutant. Determined by X-ray diffraction at 2.25 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Mus musculus, Streptomyces lividans
Chains: 3
Atoms: 4,386
Mol. weight: 58.48 kDa
Ligands: F09, 1EM
Released: 6 Dec 2017

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

Secondary structure: helices and β-sheets

5VKH contains 16 α-helices and 43 β-strands across 3 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-12	4	2
β-strand	18-24	7	1
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	107-108	2	2
β-strand	112-116	5	2
α-helix	120-121	2
β-strand	122	1	3
α-helix	123-124	2
β-strand	125-129	5	4
β-strand	140-150	11	4
β-strand	151	1	3
β-strand	156-159	4	5
α-helix	160-162	3
β-strand	164	1	5
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	180-189	10	4
α-helix	190-192	3
β-strand	199-204	6	5
α-helix	205-207	3
β-strand	209-214	6	5

Chain B: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-155	3	10
β-strand	159-163	5	9
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-198	8	10
β-strand	201-210	10	10

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	24-51	28
α-helix	62-73	12
α-helix	86-121	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody Heavy Chain	A	protein	219	Mus musculus
Antibody Light Chain	B	protein	212	Mus musculus
pH-gated potassium channel KcsA	C	protein	103	Streptomyces lividans	P0A334 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VKH_1 Antibody Heavy Chain (chains A)
QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANY
NEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 2 (B), FASTA

>5VKH_2 Antibody Light Chain (chains B)
DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPS
RFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 3 (C), FASTA

>5VKH_3 pH-gated potassium channel KcsA (chains C)
SALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDL
APVTLWGRCVAVVVMVAGITSAGLVTAALATWFVGREQERRGH

Ligands and cofactors

ID	Name	Formula	Copies
F09	Nonan-1-ol	C9 H20 O	1
1EM	(1S)-2-hydroxy-1-[(nonanoyloxy)methyl]ethyl myristate	C26 H50 O5	1

Water and common crystallization additives (K) are not listed.

Primary citation

The gating cycle of a K+ channel at atomic resolution. Cuello, L.G., Cortes, D.M., Perozo, E. Elife (2017) 6. DOI 10.7554/eLife.28032 · PubMed

Other PDB entries of the same protein (UniProt P0A334 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2IH3 1.72 Å, Ion selectivity in a semi-synthetic K+ channel locked in the conductive conformation
1R3J 1.9 Å, potassium channel KcsA-Fab complex in high concentration of Tl+
2HVK 1.9 Å, crystal structure of the KcsA-Fab-TBA complex in high K+
1K4C 2.0 Å, Potassium Channel KcsA-Fab complex in high concentration of K+
2P7T 2.05 Å, Crystal Structure of KcsA mutant
6PA0 2.05 Å, Structure of the G77A mutant in Sodium Chloride
4MSW 2.06 Å, Y78 ester mutant of KcsA in high K+
6NFU 2.09 Å, Structure of the KcsA-G77A mutant or the 2,4-ion bound configuration of a K+ channel…
6NFV 2.13 Å, Structure of the KcsA-G77C mutant or the 2,4-ion bound configuration of a K+ channel…
2H8P 2.25 Å, Structure of a K channel with an amide to ester substitution in the selectivity filter
5VK6 2.25 Å, Open conformation of KcsA non-inactivating E71A mutant
1K4D 2.3 Å, Potassium Channel KcsA-Fab complex in low concentration of K+

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