2YDQ: CpOGA D298N

CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: CLOSTRIDIUM PERFRINGENS, HOMO SAPIENS
Chains: 2
Atoms: 4,753
Mol. weight: 69.16 kDa
Ligands: NAG, CD
Released: 14 Mar 2012

Explore 2YDQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YDQ contains 31 α-helices and 25 β-strands across 1 chain. 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: 31 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	49-50	2
β-strand	52-55	4	1
β-strand	60-61	2	2
α-helix	62-63	2
β-strand	65-66	2	3
β-strand	67-69	3	1
α-helix	76-88	13
β-strand	92-93	2	3
α-helix	94	1
β-strand	103-108	6	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	4
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	4
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	4
α-helix	267-285	19
β-strand	291-295	5	4
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	4
α-helix	337-340	4
β-strand	341-342	2	5
β-strand	345-346	2	5
α-helix	348-356	9
β-strand	362-365	4	4
β-strand	375	1	6
α-helix	377-386	10
β-strand	391-395	5	4
β-strand	415	1	6
α-helix	419-421	3
β-strand	423-428	6	4
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	7
β-strand	492-493	2	7
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	611-616	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-glcnacase nagj	A	protein	590	CLOSTRIDIUM PERFRINGENS	Q0TR53 (AlphaFold model)
Bifunctional protein ncoat	T	protein	7	HOMO SAPIENS	O60502 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YDQ_1 O-GLCNACASE NAGJ (chains A)
GSVGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTA
NNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKD
GDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGEN
KLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGD
AGEEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPL
ITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYD
RNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYS
WNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDEL
WNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKAS
LDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALS

Sequence of entity 2 (T), FASTA

>2YDQ_2 BIFUNCTIONAL PROTEIN NCOAT (chains T)
VAHSGAK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CD	Cadmium ion	Cd	19

Primary citation

Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition. Schimpl, M., Borodkin, V.S., Gray, L.J. et al. Chem Biol (2012) 19:173. DOI 10.1016/J.CHEMBIOL.2012.01.011 · 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
7KHV 2.3 Å, Cpoga in complex with ligand 54
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…

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