5UHP: Core catalytic domain of human O-GlcNAcase

Crystal structure of the core catalytic domain of human O-GlcNAcase. Determined by X-ray diffraction at 2.79 Å resolution. Released 29 Mar 2017.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,813
Mol. weight: 249.99 kDa
Released: 29 Mar 2017

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

Secondary structure: helices and β-sheets

5UHP contains 79 α-helices and 44 β-strands across 8 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: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	1
α-helix	71-74	4
α-helix	75-87	13
β-strand	92-95	4	1
α-helix	109-112	4
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	246-249	4	1
α-helix	261-268	8
β-strand	276-279	4	1
α-helix	301-306	6
β-strand	309-312	4	1
α-helix	318-321	4
α-helix	322-333	12
α-helix	376-391	16
β-strand	395	1	2

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	3
α-helix	72-74	3
α-helix	75-87	13
β-strand	92-95	4	3
α-helix	109-112	4
α-helix	113-128	16
β-strand	132-137	6	3
α-helix	148-162	15
β-strand	168-172	5	3
α-helix	182-187	6
α-helix	191-205	15
β-strand	212-215	4	3
β-strand	220	1	4
α-helix	221-223	3
α-helix	232-240	9
β-strand	245-249	5	3
β-strand	251	1	4
β-strand	259	1	5
α-helix	261-271	11
α-helix	274-275	2
β-strand	276-279	4	3
β-strand	299	1	5
α-helix	301-306	6
β-strand	309-312	4	3
α-helix	318-321	4
α-helix	322-333	12
α-helix	376-392	17
β-strand	395	1	6

Chain C: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	7
α-helix	75-87	13
β-strand	92-95	4	7
α-helix	110-111	2
α-helix	113-128	16
β-strand	132-137	6	7
α-helix	148-163	16
β-strand	168-172	5	7
α-helix	182-185	4
α-helix	191-205	15
β-strand	212-215	4	7
α-helix	232-240	9
β-strand	246-249	4	7
α-helix	261-271	11
α-helix	274-275	2
β-strand	276-279	4	7
α-helix	301-306	6
β-strand	309-312	4	7
α-helix	318-321	4
α-helix	322-334	13
α-helix	376-390	15

Chain D: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	8
α-helix	71-73	3
α-helix	75-87	13
β-strand	92-95	4	8
α-helix	110-112	3
α-helix	113-128	16
α-helix	131	1
β-strand	132-137	6	8
α-helix	148-162	15
β-strand	168-172	5	8
α-helix	182-185	4
α-helix	191-205	15
β-strand	212-215	4	8
α-helix	221-223	3
α-helix	232-240	9
β-strand	246-249	4	8
α-helix	261-271	11
β-strand	276-279	4	8
α-helix	301-306	6
β-strand	309-312	4	8
α-helix	318-321	4
α-helix	322-333	12
α-helix	376-388	13
α-helix	389-391	3

Chain E: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	555-564	10
α-helix	573-586	14
α-helix	604-629	26
α-helix	635-655	21
α-helix	684-690	7

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	555-564	10
β-strand	567	1	9
β-strand	570	1	9
α-helix	573-586	14
α-helix	604-629	26
β-strand	633	1	2
α-helix	634-659	26
α-helix	685-690	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	555-564	10
β-strand	567	1	10
β-strand	570	1	10
α-helix	573-586	14
α-helix	604-629	26
β-strand	633	1	6
α-helix	634-649	16
α-helix	652-658	7
α-helix	684-690	7

Chain H: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	555-564	10
α-helix	573-586	14
α-helix	604-629	26
α-helix	634-659	26
α-helix	684-690	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-GlcNAcase TIM-barrel domain	A, B, C, D	protein	388	Homo sapiens	O60502 (AlphaFold model)
O-GlcNAcase stalk domain	E, F, G, H	protein	161	Homo sapiens	O60502 (AlphaFold model)

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

>5UHP_1 O-GlcNAcase TIM-barrel domain (chains A, B, C, D)
GESELSSNPAASAGASLEPPAAPAPGEDNPAGAGGAAVAGAAGGARRFLCGVVEGFYGRP
WVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIE
FIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFA
HAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGP
KVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLT
NPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIKLENEGSDEDIETDV
LYSPQMALKLALTEWLQEFGVPHQYSSR

Sequence of entity 2 (E, F, G, H), FASTA

>5UHP_2 O-GlcNAcase stalk domain (chains E, F, G, H)
MTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAA
KFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFL
IGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQPHHHHHHHH

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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