6OCH: VASH1-SVBP complex

Crystal structure of VASH1-SVBP complex bound with parthenolide. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,112
Mol. weight: 64.09 kDa
Ligands: M4Y
Released: 26 Jun 2019

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

Secondary structure: helices and β-sheets

6OCH contains 30 α-helices and 22 β-strands across 4 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	62	1	1
α-helix	69-70	2
α-helix	71-84	14
α-helix	89-95	7
α-helix	107-110	4
α-helix	118-131	14
β-strand	134	1	2
β-strand	140	1	1
α-helix	150-163	14
β-strand	167	1	2
α-helix	169-178	10
β-strand	186-197	12	3
β-strand	200-211	12	3
β-strand	214-218	5	3
α-helix	224-226	3
β-strand	229-233	5	3
α-helix	236-249	14
α-helix	252	1
β-strand	253-259	7	3
α-helix	261-264	4
α-helix	272-273	2
β-strand	278-281	4	3
α-helix	282-285	4
α-helix	287-301	15

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-51	25

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	62	1	4
α-helix	69-70	2
α-helix	71-84	14
α-helix	89-95	7
α-helix	107-110	4
α-helix	118-132	15
β-strand	134	1	5
β-strand	140	1	4
β-strand	149	1	6
α-helix	150-163	14
β-strand	167	1	5
α-helix	169-180	12
β-strand	186-197	12	7
β-strand	200-211	12	7
β-strand	214-218	5	7
α-helix	224-226	3
β-strand	229-233	5	7
α-helix	236-249	14
α-helix	252	1
β-strand	253-259	7	7
α-helix	260-264	5
α-helix	271	1
β-strand	272	1	6
α-helix	273	1
β-strand	278-281	4	7
α-helix	282-300	19

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-50	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 1	A, C	protein	242	Homo sapiens	Q7L8A9 (AlphaFold model)
Small vasohibin-binding protein	B, D	protein	28	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OCH_1 Tubulinyl-Tyr carboxypeptidase 1 (chains A, C)
FVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPVPE
RLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLT
NSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELV
LDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHARD
MR

Sequence of entity 2 (B, D), FASTA

>6OCH_2 Small vasohibin-binding protein (chains B, D)
KSAQQELKQRQRAEIYALNRVMTELEQQ

Ligands and cofactors

ID	Name	Formula	Copies
M4Y	parthenolide	C15 H20 O3	2

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

Primary citation

Structural basis of tubulin detyrosination by vasohibins. Li, F., Hu, Y., Qi, S. et al. Nat Struct Mol Biol (2019) 26:583-591. DOI 10.1038/s41594-019-0242-x · PubMed

Other PDB entries of the same protein (UniProt Q7L8A9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6J7B 1.62 Å, Crystal structure of VASH1-SVBP in complex with epoY
6OCG 1.83 Å, Crystal structure of VASH1-SVBP complex bound with EpoY
6J8O 1.85 Å, Structure of a hypothetical protease
6J8N 1.95 Å, Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1
6J4U 2.0 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6NVQ 2.1 Å, Crystal structure of the VASH1-SVBP complex
6OCF 2.1 Å, The crystal structure of VASH1-SVBP complex
6K81 2.28 Å, Crystal structure of human VASH1-SVBP complex
6J8F 2.28 Å, Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin
6LPG 2.3 Å, human VASH1-SVBP complex
6J9H 2.31 Å, Crystal structure of SVBP-VASH1 complex
6WSL 3.1 Å, Cryo-EM structure of VASH1-SVBP bound to microtubules

Browse structure collections

About this viewer

MolViewer shows 6OCH 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.