5NVG: Thr12 Phosphorylated Ubiquitin

Thr12 Phosphorylated Ubiquitin. Determined by X-ray diffraction at 1.07 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 1.07 Å
Organism: Homo sapiens
Chains: 1
Atoms: 825
Mol. weight: 8.86 kDa
Ligands: PO4
Released: 31 May 2017

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

Secondary structure: helices and β-sheets

5NVG contains 4 α-helices and 7 β-strands across 1 chain. 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-B	A	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NVG_1 Polyubiquitin-B (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing. Zhang, M.S., Brunner, S.F., Huguenin-Dezot, N. et al. Nat Methods (2017) 14:729-736. DOI 10.1038/nmeth.4302 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
5KYC 1.43 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin…

Browse structure collections

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