2CBI: Hyaluronidase

Name: PDB 2CBI: Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase
Published: 2006-02-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase. Determined by X-ray diffraction at 2.25 Å resolution. Released 13 Feb 2006.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: CLOSTRIDIUM PERFRINGENS
Chains: 2
Atoms: 9,931
Mol. weight: 134.58 kDa
Ligands: GBL, ZN
Released: 13 Feb 2006

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

Secondary structure: helices and β-sheets

2CBI contains 69 α-helices and 46 β-strands across 2 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: 35 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	49-50	2
β-strand	52-61	10	1
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	1
β-strand	167-175	9	1
β-strand	181-185	5	2
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	2
α-helix	221-223	3
α-helix	230-232	3
α-helix	233-235	3
α-helix	236-248	13
β-strand	252-257	6	2
α-helix	259-261	3
α-helix	267-285	19
β-strand	291-295	5	2
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	2
α-helix	337-340	4
β-strand	341-342	2	3
β-strand	345-346	2	3
α-helix	348-356	9
β-strand	362-365	4	2
β-strand	375	1	4
α-helix	377-387	11
β-strand	391-395	5	2
β-strand	415	1	4
α-helix	419-421	3
β-strand	423-428	6	2
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	5
β-strand	492-493	2	5
α-helix	496	1
α-helix	499-512	14
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-598	19
α-helix	606-610	5
α-helix	611-618	8
α-helix	621-623	3

Chain B: 34 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	49-50	2
β-strand	52-61	10	6
α-helix	62-63	2
β-strand	65-69	5	6
α-helix	76-88	13
β-strand	92-93	2	6
α-helix	94	1
β-strand	102-108	7	6
α-helix	114-120	7
β-strand	133-138	6	6
β-strand	141-146	6	6
α-helix	149-162	14
β-strand	164	1	6
β-strand	167-175	9	6
β-strand	181-185	5	7
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	7
α-helix	221-223	3
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	7
α-helix	267-285	19
β-strand	291-295	5	7
α-helix	304-314	11
α-helix	315-319	5
α-helix	320-322	3
α-helix	326-328	3
β-strand	329-331	3	7
α-helix	337-340	4
β-strand	341-342	2	8
β-strand	345-346	2	8
α-helix	348-356	9
β-strand	362-365	4	7
β-strand	375	1	9
α-helix	377-387	11
β-strand	391-395	5	7
β-strand	406	1	10
β-strand	415	1	9
α-helix	419-421	3
β-strand	423-428	6	7
α-helix	434-449	16
α-helix	451-453	3
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	11
β-strand	492-493	2	11
α-helix	496	1
α-helix	499-512	14
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
β-strand	603	1	10
α-helix	606-610	5
α-helix	611-617	7
α-helix	621-623	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hyaluronidase	A, B	protein	594	CLOSTRIDIUM PERFRINGENS	Q0TR53 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2CBI_1 HYALURONIDASE (chains A, B)
VGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANN
IEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGD
GTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKL
NTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAG
EEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLIT
VPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRN
MAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWN
MDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWN
KLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLD
MIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

Ligands and cofactors

ID	Name	Formula	Copies
GBL	Gamma-butyrolactone	C4 H6 O2	2
ZN	Zinc ion	Zn	11

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

Primary citation

Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis. Rao, F.V., Dorfmueller, H.C., Villa, F. et al. EMBO J (2006) 25:1569-1578. DOI 10.1038/sj.emboj.7601026 · 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
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…
2J1E 2.4 Å, High Resolution Crystal Structure of CBM32 from a N-acetyl-beta- hexosaminidase in…

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