5UHK: Core catalytic domain of Human O-GlcNAcase

Crystal structure of the core catalytic domain of Human O-GlcNAcase. Determined by X-ray diffraction at 2.97 Å resolution. Released 29 Mar 2017.

Method: X-ray diffraction
Resolution: 2.97 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,936
Mol. weight: 117.82 kDa
Released: 29 Mar 2017

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

Secondary structure: helices and β-sheets

5UHK contains 46 α-helices and 24 β-strands across 4 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: 16 helices, 10 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	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	191-205	15
β-strand	212-215	4	1
α-helix	221-223	3
α-helix	232-240	9
β-strand	245-249	5	1
β-strand	259	1	2
α-helix	261-271	11
β-strand	276-279	4	1
α-helix	285-287	3
α-helix	295	1
β-strand	299	1	2
α-helix	301-306	6
β-strand	309-312	4	1
α-helix	318-321	4
α-helix	322-334	13
α-helix	376-388	13

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	545-548	4
α-helix	551-553	3
α-helix	555-564	10
β-strand	567	1	3
β-strand	570	1	3
α-helix	573-586	14
α-helix	607-630	24
α-helix	634-638	5
α-helix	641-661	21
α-helix	684-691	8

Chain C: 15 helices, 10 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	113-128	16
β-strand	132-137	6	4
α-helix	148-163	16
β-strand	168-172	5	4
α-helix	180-181	2
α-helix	182-187	6
α-helix	191-205	15
β-strand	212-215	4	4
α-helix	232-240	9
β-strand	246-249	4	4
β-strand	259	1	5
α-helix	261-271	11
β-strand	276-279	4	4
α-helix	285-287	3
α-helix	295-296	2
β-strand	299	1	5
α-helix	301-306	6
β-strand	309-312	4	4
α-helix	318-321	4
α-helix	322-333	12
α-helix	376-387	12

Chain D: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	544-547	4
α-helix	550-554	5
α-helix	555-564	10
β-strand	567	1	6
β-strand	570	1	6
α-helix	573-586	14
α-helix	606-630	25
α-helix	634-660	27
α-helix	684-691	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-GlcNAcase TIM-barrel domain	A, C	protein	345	Homo sapiens	O60502 (AlphaFold model)
O-GlcNAcase stalk domain	B, D	protein	163	Homo sapiens	O60502 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5UHK_1 O-GlcNAcase TIM-barrel domain (chains A, C)
GARRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEE
AEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDD
IDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLR
TVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGP
YKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSI
QIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSR

Sequence of entity 2 (B, D), FASTA

>5UHK_2 O-GlcNAcase stalk domain (chains B, D)
MEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSE
KIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLG
CRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQP

Primary citation

Crystal structure of the core catalytic domain of human O-GlcNAcase and molecular basis of activity and inhibition. Elsen, N.L., Patel, S.B., Ford, R.E. et al. To be published.

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

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