5DIY: PDB entry 5DIY

Name: PDB 5DIY: Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N
Published: 2015-10-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N. Determined by X-ray diffraction at 2.06 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 2.06 Å
Organisms: Homo sapiens, Thermobaculum terrenum
Chains: 4
Atoms: 8,034
Mol. weight: 112.9 kDa
Ligands: NAG
Released: 28 Oct 2015

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

Secondary structure: helices and β-sheets

5DIY contains 53 α-helices and 30 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: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
α-helix	17-19	3
α-helix	20-32	13
β-strand	37-40	4	1
α-helix	46-48	3
α-helix	55-57	3
α-helix	58-73	16
β-strand	77-82	6	1
α-helix	93-108	16
β-strand	113-117	5	1
α-helix	128-133	6
α-helix	137-153	17
β-strand	160-164	5	1
β-strand	169	1	2
α-helix	175-183	9
β-strand	189-192	4	1
β-strand	194	1	2
β-strand	202	1	3
α-helix	204-214	11
β-strand	218-222	5	1
α-helix	229-231	3
α-helix	239-240	2
β-strand	243	1	3
α-helix	247-249	3
β-strand	251-256	6	1
α-helix	262-277	16
α-helix	284-296	13
α-helix	298-300	3
α-helix	301-308	8
β-strand	314	1	4
β-strand	317	1	4
α-helix	321	1
α-helix	322-336	15
α-helix	340-362	23
α-helix	367-371	5
α-helix	373-398	26
α-helix	412-428	17
α-helix	429-431	3
α-helix	440-451	12
α-helix	453-459	7
α-helix	466	1
β-strand	467	1	5
β-strand	471	1	5

Chain B: 26 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	6
α-helix	17-19	3
α-helix	20-32	13
β-strand	37-40	4	6
α-helix	55-57	3
α-helix	58-73	16
β-strand	77-82	6	6
α-helix	93-108	16
β-strand	113-117	5	6
α-helix	128-133	6
α-helix	137-153	17
β-strand	160-164	5	6
β-strand	169	1	7
α-helix	175-183	9
β-strand	189-192	4	6
β-strand	194	1	7
β-strand	202	1	8
α-helix	204-214	11
α-helix	217	1
β-strand	218-222	5	6
α-helix	229-231	3
α-helix	239-240	2
β-strand	243	1	8
α-helix	247-249	3
β-strand	251-256	6	6
α-helix	262-277	16
α-helix	284-296	13
α-helix	298-300	3
α-helix	301-308	8
α-helix	322-336	15
α-helix	340-362	23
α-helix	367-371	5
α-helix	373-396	24
α-helix	409-428	20
α-helix	429-431	3
α-helix	440-451	12
α-helix	453-459	7
α-helix	466	1
β-strand	467	1	9
β-strand	471	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TGF-beta-activated kinase 1 and MAP3K7-binding protein 1	P, Q	protein	7	Homo sapiens	Q15750 (AlphaFold model)
Hyaluronidase	A, B	protein	474	Thermobaculum terrenum	D1CDN2 (AlphaFold model)

Sequence of entity 1 (P, Q), FASTA

>5DIY_1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 (chains P, Q)
VPYSSAQ

Sequence of entity 2 (A, B), FASTA

>5DIY_2 Hyaluronidase (chains A, B)
MEYFRYRGIIEGFYGKPWEHQERLDMFEFMQANNLNAYIYAPKQDLYHRELWREPYKEEQ
LQLFKELIEKAGSCGINFTFAISPGLSLVYSSEEELETLIRKITPFLEMGVHSIGIFFDN
VPFDLIHEEDRNSYSNLAEAQADFLTRVLQRLESTISTPQIIMCPTFYCNDPNLEYLRIL
GQRLPKNIDVFWTGPNVCSHEITTSHMQEVQKSLQRPATLWDNYPVNDGGMMPELHIGPY
DHRDPELHTHVVGIYANPMALPEASKLPLYTFAQYLNSPSQYNPQDSWRQAVSTLLGEDN
LSAMEKFYQSNTISCLEPEEPAYLTNLFKKVQEDFASFRFEQGLRTLREEIISMQTTYSR
LSTQDSKFFWEIRPWLEEYKLWTDYLDQAMITFSNLFTGFFTADEEQARESLQKALQGRT
YLREVLKDAVDFRTRVCGDVVRNFLQQVLRSTVSIELQAEGKEWTALPPGIVRD

Ligands and cofactors

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

Primary citation

Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum. Ostrowski, A., Gundogdu, M., Ferenbach, A.T. et al. J Biol Chem (2015) 290:30291-30305. DOI 10.1074/jbc.M115.689596 · PubMed

Other PDB entries of the same protein (UniProt Q15750 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NTH 1.97 Å, Structure of TAK1 in complex with compound 54
7NTI 1.98 Å, Structure of TAK1 in complex with compound 22
5JGA 2.0 Å, Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 11c
5V5N 2.01 Å, Crystal structure of Takinib bound to TAK1
8GW3 2.05 Å, Crystal structure of human TAK1 kinase domain fused with TAB1
5E7R 2.11 Å, Crystal structure of TL10-81 bound to TAK1-TAB1
4GS6 2.2 Å, Irreversible Inhibition of TAK1 Kinase by 5Z-7-Oxozeaenol
2J4O 2.25 Å, Structure of TAB1
2POM 2.27 Å, TAB1 with manganese ion
5JH6 2.37 Å, Crystal structure of TL10-92 bound to TAK1-TAB1
5J7S 2.37 Å, Crystal structure of SM1-71 bound to TAK1-TAB1
5JK3 2.37 Å, Crystal structure of TL11-128 bound to TAK1-TAB1

Browse structure collections

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