7KHV: Cpoga

Cpoga in complex with ligand 54. Determined by X-ray diffraction at 2.3 Å resolution. Released 2 Dec 2020.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Clostridium perfringens
Chains: 6
Atoms: 29,407
Mol. weight: 406.21 kDa
Ligands: X1A, CA
Released: 2 Dec 2020

Explore 7KHV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KHV contains 195 α-helices and 139 β-strands across 6 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: 33 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	49-50	2
β-strand	52-55	4	1
β-strand	60-61	2	2
α-helix	62-63	2
β-strand	65-69	5	1
α-helix	76-88	13
β-strand	92-93	2	1
α-helix	94	1
β-strand	102-108	7	1
α-helix	114-120	7
α-helix	129	1
β-strand	133-138	6	1
β-strand	141-146	6	1
α-helix	149-162	14
β-strand	164	1	2
β-strand	167-168	2	2
β-strand	171-175	5	1
β-strand	181-186	6	3
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	3
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	3
α-helix	267-285	19
β-strand	291-295	5	3
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	325-328	4
β-strand	329-331	3	3
α-helix	337-340	4
β-strand	341-342	2	4
β-strand	345-346	2	4
α-helix	348-356	9
β-strand	362-365	4	3
β-strand	375	1	5
α-helix	377-387	11
β-strand	391-395	5	3
β-strand	415	1	5
α-helix	419-421	3
β-strand	423-428	6	3
α-helix	434-449	16
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	6
β-strand	492-493	2	6
α-helix	496	1
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Chain B: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	49-50	2
β-strand	52-55	4	7
β-strand	60-61	2	8
α-helix	62-63	2
β-strand	65-69	5	7
α-helix	76-88	13
β-strand	92-93	2	7
α-helix	94	1
β-strand	102-108	7	7
α-helix	114-120	7
β-strand	133-138	6	7
β-strand	141-146	6	7
α-helix	149-162	14
β-strand	164	1	8
β-strand	167-168	2	8
β-strand	171-175	5	7
β-strand	181-186	6	9
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	9
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	9
α-helix	267-285	19
β-strand	291-295	5	9
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	326-328	3
β-strand	329-331	3	9
α-helix	337-340	4
β-strand	341-342	2	10
β-strand	345-346	2	10
α-helix	348-356	9
β-strand	362-365	4	9
β-strand	375	1	11
α-helix	377-387	11
β-strand	391-395	5	9
β-strand	415	1	11
α-helix	419-421	3
β-strand	423-428	6	9
α-helix	434-449	16
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	12
β-strand	492-493	2	12
α-helix	495-496	2
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Chain C: 33 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	49-50	2
β-strand	52-55	4	13
β-strand	60-61	2	14
α-helix	62-63	2
β-strand	65-69	5	13
α-helix	76-88	13
β-strand	92-93	2	13
α-helix	94	1
β-strand	102-108	7	13
α-helix	116-120	5
α-helix	129	1
β-strand	133-138	6	13
β-strand	141-146	6	13
α-helix	149-162	14
β-strand	164	1	14
β-strand	167-168	2	14
β-strand	171-175	5	13
β-strand	181-186	6	15
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	15
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	15
α-helix	267-285	19
β-strand	291-295	5	15
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	326-328	3
β-strand	329-331	3	15
α-helix	337-340	4
β-strand	341-342	2	16
β-strand	345-346	2	16
α-helix	348-356	9
β-strand	362-365	4	15
β-strand	375	1	17
α-helix	377-387	11
β-strand	391-395	5	15
α-helix	410-412	3
β-strand	415	1	17
α-helix	419-421	3
β-strand	423-428	6	15
α-helix	434-449	16
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	18
β-strand	492-493	2	18
α-helix	496	1
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Chain D: 34 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	49-50	2
β-strand	52-55	4	19
β-strand	60-61	2	20
α-helix	62-63	2
β-strand	65-69	5	19
α-helix	76-88	13
β-strand	92-93	2	19
α-helix	94	1
β-strand	102-108	7	19
α-helix	114-120	7
α-helix	129	1
β-strand	133-137	5	19
β-strand	141-146	6	19
α-helix	149-162	14
β-strand	164	1	20
β-strand	167-168	2	20
β-strand	171-175	5	19
β-strand	181-186	6	21
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	21
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	21
α-helix	267-285	19
β-strand	291-295	5	21
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	325-328	4
β-strand	329-331	3	21
α-helix	337-340	4
β-strand	341-342	2	22
β-strand	345-346	2	22
α-helix	348-356	9
β-strand	362-365	4	21
β-strand	375	1	23
α-helix	377-387	11
β-strand	391-395	5	21
α-helix	410-412	3
β-strand	415	1	23
α-helix	419-421	3
β-strand	423-428	6	21
α-helix	438-449	12
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	24
β-strand	492-493	2	24
α-helix	496	1
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Chain E: 34 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	49-50	2
β-strand	52-55	4	25
β-strand	60-61	2	26
α-helix	62-63	2
β-strand	65-69	5	25
α-helix	76-88	13
β-strand	92-93	2	25
α-helix	94	1
β-strand	102-108	7	25
α-helix	114-120	7
α-helix	129	1
β-strand	133-138	6	25
β-strand	141-146	6	25
α-helix	149-162	14
β-strand	164	1	26
β-strand	167-168	2	26
β-strand	171-175	5	25
β-strand	181-186	6	27
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	27
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	27
α-helix	267-285	19
β-strand	291-295	5	27
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	326-328	3
β-strand	329-331	3	27
α-helix	337-340	4
β-strand	341-342	2	28
β-strand	345-346	2	28
α-helix	348-356	9
β-strand	362-365	4	27
β-strand	375	1	29
α-helix	377-387	11
β-strand	391-395	5	27
α-helix	410-412	3
β-strand	415	1	29
α-helix	419-421	3
β-strand	423-428	6	27
α-helix	434-449	16
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	30
β-strand	492-493	2	30
α-helix	496	1
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Chain F: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	49-50	2
β-strand	52-55	4	31
α-helix	76-88	13
α-helix	92-94	3
β-strand	108	1	31
α-helix	129	1
β-strand	133-134	2	31
β-strand	145-146	2	31
α-helix	149-162	14
β-strand	171-175	5	31
β-strand	181-186	6	32
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	32
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	32
α-helix	267-285	19
β-strand	291-295	5	32
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	325-328	4
β-strand	329-331	3	32
α-helix	337-340	4
β-strand	341-342	2	33
β-strand	345-346	2	33
α-helix	348-356	9
β-strand	362-365	4	32
β-strand	375	1	34
α-helix	377-387	11
β-strand	391-395	5	32
β-strand	415	1	34
α-helix	419-421	3
β-strand	423-428	6	32
α-helix	434-449	16
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	35
β-strand	492-493	2	35
α-helix	496	1
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-GlcNAcase NagJ	A, B, C, D, E, F	protein	594	Clostridium perfringens	Q0TR53 (AlphaFold model)

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

>7KHV_1 O-GlcNAcase NagJ (chains A, B, C, D, E, F)
VGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANN
IEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGD
GTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKL
NTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAG
EEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLIT
CPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRN
MAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWN
MDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWN
KLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLD
MIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

Ligands and cofactors

ID	Name	Formula	Copies
X1A	N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octa…	C18 H22 N8 O S	6
CA	Calcium ion	Ca	3

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

Diazaspirononane Nonsaccharide Inhibitors of O-GlcNAcase (OGA) for the Treatment of Neurodegenerative Disorders. Martinez-Viturro, C.M., Trabanco, A.A., Royes, J. et al. J Med Chem (2020) 63:14017-14044. DOI 10.1021/acs.jmedchem.0c01479 · PubMed

Other PDB entries of the same protein (UniProt Q0TR53 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J1A 1.49 Å, Structure of CBM32 from Clostridium perfringens beta-N- acetylhexosaminidase GH84C in…
2OZN 1.6 Å, The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens
2W1N 1.8 Å, cohesin and fibronectin type-III double module construct from the Clostridium…
2V5C 2.1 Å, Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure
2VUR 2.2 Å, Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death
2CBI 2.25 Å, Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue…
2X0Y 2.25 Å, Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds
2J62 2.26 Å, Structure of a bacterial O-glcnacase in complex with glcnacstatin
2J7M 2.3 Å, Characterization of a Family 32 CBM
2WB5 2.31 Å, GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular…
2CBJ 2.35 Å, Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue…
2J1E 2.4 Å, High Resolution Crystal Structure of CBM32 from a N-acetyl-beta- hexosaminidase in…

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