6E2B: Ubiquitin

Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3). Determined by X-ray diffraction at 1.45 Å resolution. Released 14 Nov 2018.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Bos taurus
Chains: 6
Atoms: 4,495
Mol. weight: 54.72 kDa
Ligands: PT7
Released: 14 Nov 2018

Explore 6E2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E2B contains 24 α-helices and 42 β-strands across 6 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	13-16	4	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

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	13-16	4	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50	1
β-strand	55	1	4
α-helix	56-59	4
β-strand	66-71	6	3

Chain E: 3 helices, 7 β-strands

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

Chains G and I: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7

Chain P: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
α-helix	11	1
β-strand	12-16	5	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	55	1	12
α-helix	57-59	3
β-strand	66-71	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, C, E, G, I, P	protein	76	Bos taurus	P62992 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, P), FASTA

>6E2B_1 Ubiquitin (chains A, C, E, G, I, P)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
PT7	chloro[2-(pyridin-2-yl-kappaN)phenyl-kappaC~1~](triphenyl-lambda~5~-phosphanyl)…	C29 H23 Cl N P Pt	3

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Reactions of Cyclometalated Platinum(II) [Pt(N∧C)(PR3)Cl] Complexes with Imidazole and Imidazole-Containing Biomolecules: Fine-Tuning of Reactivity and Photophysical Properties via Ligand Design. Solomatina, A.I., Chelushkin, P.S., Abakumova, T.O. et al. Inorg Chem (2019) 58:204-217. DOI 10.1021/acs.inorgchem.8b02204 · PubMed

Other PDB entries of the same protein (UniProt P62992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q01 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2
5XVE 1.24 Å, Crystal structure of human USP2 C276S mutant in complex with ubiquitin
4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
4Y1H 1.4 Å, Crystal structure of K33 linked tri-Ubiquitin
5XU8 1.81 Å, Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine
5MN9 2.05 Å, Crystal structure of MINDY-1 tMIU in complex with K48-diUb
5BZ0 2.1 Å, Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin
7F0U 2.2 Å, porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono…
4Z9S 2.3 Å, Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
5JQS 2.65 Å, Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
6DJW 3.8 Å, Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex

Browse structure collections

About this viewer

MolViewer shows 6E2B directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.