5M7U: Protein O-GlcNAcase

Name: PDB 5M7U: Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor
Published: 2017-03-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Mar 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,462
Mol. weight: 206.82 kDa
Ligands: XHA
Released: 29 Mar 2017

Explore 5M7U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M7U contains 51 α-helices and 20 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: 26 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	179-181	3
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	261-271	11
α-helix	274-275	2
β-strand	276-279	4	1
α-helix	295-296	2
α-helix	301-306	6
β-strand	309-312	4	1
α-helix	318-321	4
α-helix	322-334	13
α-helix	376-391	16
α-helix	545-547	3
α-helix	552-553	2
α-helix	555-564	10
β-strand	567	1	2
β-strand	570	1	2
α-helix	573-587	15
α-helix	589-591	3
α-helix	602-628	27
α-helix	634-661	28
α-helix	678-680	3
α-helix	684-690	7

Chain B: 25 helices, 10 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	110-112	3
α-helix	113-128	16
β-strand	132-137	6	3
α-helix	148-162	15
β-strand	168-172	5	3
α-helix	179-181	3
α-helix	182-187	6
α-helix	191-205	15
β-strand	212-215	4	3
α-helix	221-223	3
α-helix	232-240	9
β-strand	246-249	4	3
α-helix	261-271	11
α-helix	274-275	2
β-strand	276-279	4	3
α-helix	295-296	2
α-helix	301-306	6
β-strand	309-312	4	3
α-helix	318-321	4
α-helix	322-334	13
α-helix	376-391	16
α-helix	551-553	3
α-helix	555-564	10
β-strand	567	1	4
β-strand	570	1	4
α-helix	573-587	15
α-helix	589-591	3
α-helix	602-628	27
α-helix	634-661	28
α-helix	678-680	3
α-helix	685-690	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-GlcNAcase	A, B	protein	916	Homo sapiens	O60502 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5M7U_1 Protein O-GlcNAcase (chains A, B)
MVQKESQATLEERESELSSNPAASAGASLEPPAAPAPGEDNPAGAGGAAVAGAAGGARRF
LCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLM
TLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNM
CAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEK
LLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRS
TELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIKLE
NEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRQVAHSGAKASVVDGTPLVAA
PSLNATTVVTTVYQEPIMSQGAALSGEPTTLTKEEEKKQPDEEPMDMVVEKQEETDHKND
NQILSEIVEAKMAEELKPMDTDKESIAESKSPEMSMQEDCISDIAPMQTDEQTNKEQFVP
GPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKD
SEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQW
LGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQPPPLTPTSKVYTIRPY
FPKDEASVYKICREMYDDGVGLPFQSQPDLIGDKLVGGLLSLSLDYCFVLEDEDGICGYA
LGTVDVTPFIKKCKISWIPFMQEKYTKPNGDKELSEAEKIMLSFHEEQEVLPETFLANFP
SLIKMDIHKKVTDPSVAKSMMACLLSSLKANGSRGAFCEVRPDDKRILEFYSKLGCFEIA
KMEGFPKDVVILGRSL

Ligands and cofactors

ID	Name	Formula	Copies
XHA	2-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-[3-[3-(trifl…	C18 H25 F3 N2 O4	2

Primary citation

Structural and functional insight into human O-GlcNAcase. Roth, C., Chan, S., Offen, W.A. et al. Nat Chem Biol (2017) 13:610-612. DOI 10.1038/nchembio.2358 · 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
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
5VVO 2.6 Å, Structural Investigations of the Substrate Specificity of Human O-GlcNAcase

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