5VVX: Protein O-GlcNAcase

Structural Investigations of the Substrate Specificity of Human O-GlcNAcase. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,104
Mol. weight: 118.78 kDa
Ligands: NAG
Released: 27 Sept 2017

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

Secondary structure: helices and β-sheets

5VVX contains 46 α-helices and 24 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: 22 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	1
α-helix	72-74	3
α-helix	75-87	13
β-strand	92-95	4	1
α-helix	101-104	4
α-helix	110-112	3
α-helix	113-128	16
β-strand	132-137	6	1
α-helix	148-162	15
β-strand	168-172	5	1
α-helix	182-187	6
α-helix	191-206	16
β-strand	212-215	4	1
α-helix	221-223	3
α-helix	232-240	9
β-strand	246-249	4	1
β-strand	259	1	2
α-helix	261-270	10
β-strand	276-279	4	1
α-helix	295-296	2
β-strand	299	1	2
α-helix	301-306	6
β-strand	309-312	4	1
α-helix	318-321	4
α-helix	322-331	10
α-helix	376-388	13
α-helix	555-564	10
β-strand	567	1	3
β-strand	570	1	3
α-helix	573-587	15
α-helix	589-591	3
α-helix	605-629	25
α-helix	634-659	26
α-helix	684-692	9

Chain C: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	4
α-helix	72-74	3
α-helix	75-87	13
β-strand	92-95	4	4
α-helix	110-112	3
α-helix	113-128	16
β-strand	132-137	6	4
α-helix	148-162	15
β-strand	168-172	5	4
α-helix	182-187	6
α-helix	191-205	15
β-strand	212-215	4	4
α-helix	221-223	3
α-helix	232-240	9
β-strand	246-249	4	4
β-strand	259	1	5
α-helix	261-270	10
β-strand	276-279	4	4
α-helix	280-282	3
α-helix	294-295	2
β-strand	299	1	5
α-helix	301-306	6
β-strand	309-312	4	4
α-helix	318-320	3
α-helix	322-333	12
α-helix	376-389	14
α-helix	555-564	10
β-strand	567	1	6
β-strand	570	1	6
α-helix	573-587	15
α-helix	588-591	4
α-helix	605-629	25
α-helix	634-662	29
α-helix	663-666	4
α-helix	678-680	3
α-helix	684-690	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-GlcNAcase	A, C	protein	504	Homo sapiens	O60502 (AlphaFold model)
Lamin B1	B, D	protein	13	Homo sapiens	P20700 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5VVX_1 Protein O-GlcNAcase (chains A, C)
HFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQ
LMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDNIDH
NMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVG
EKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKG
RSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIK
LENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRGGGGSGGGGSVTLEDLQL
LADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGL
VMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWA
FRGGLAGEFQRLLPIDGANDLFFQ

Sequence of entity 2 (B, D), FASTA

>5VVX_2 Lamin B1 (chains B, D)
KLSPSPSSRVTVS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase. Li, B., Li, H., Hu, C.W. et al. Nat Commun (2017) 8:666-666. DOI 10.1038/s41467-017-00865-1 · PubMed

Other PDB entries of the same protein (UniProt O60502 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5UN8 2.13 Å, Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53
5M7U 2.3 Å, Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor
11LJ 2.33 Å, Human oga in complex with ligand 24
5M7R 2.35 Å, Structure of human O-GlcNAc hydrolase
5M7S 2.4 Å, Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG
7OU6 2.41 Å, Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines
5TKE 2.48 Å, Crystal Structure of Eukaryotic Hydrolase
5UN9 2.5 Å, The crystal structure of human O-GlcNAcase in complex with Thiamet-G
8P0L 2.5 Å, Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide
9BA8 2.54 Å, O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease
2YDQ 2.6 Å, CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide
5M7T 2.6 Å, Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor

Browse structure collections

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