6OCG: VASH1-SVBP complex

Crystal structure of VASH1-SVBP complex bound with EpoY. Determined by X-ray diffraction at 1.83 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,764
Mol. weight: 32.26 kDa
Ligands: BJL
Released: 26 Jun 2019

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

Secondary structure: helices and β-sheets

6OCG contains 15 α-helices and 12 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: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	1
α-helix	69-70	2
α-helix	71-84	14
α-helix	89-95	7
α-helix	104-110	7
α-helix	118-132	15
β-strand	134	1	2
β-strand	139-140	2	1
β-strand	149	1	3
α-helix	150-163	14
β-strand	167	1	2
α-helix	169-180	12
β-strand	186-197	12	4
β-strand	200-211	12	4
β-strand	214-218	5	4
α-helix	224-226	3
β-strand	229-233	5	4
α-helix	236-249	14
α-helix	252	1
β-strand	253-259	7	4
α-helix	261-264	4
α-helix	271	1
β-strand	272	1	3
α-helix	273	1
β-strand	278-281	4	4
α-helix	282-304	23

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-49	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 1	A	protein	247	Homo sapiens	Q7L8A9 (AlphaFold model)
Small vasohibin-binding protein	B	protein	26	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6OCG_1 Tubulinyl-Tyr carboxypeptidase 1 (chains A)
PFFVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPV
PERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIY
LTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSE
LVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHA
RDMRLKI

Sequence of entity 2 (B), FASTA

>6OCG_2 Small vasohibin-binding protein (chains B)
SAQQELKQRQRAEIYALNRVMTELEQ

Ligands and cofactors

ID	Name	Formula	Copies
BJL	N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine	C15 H19 N O7	1

Water and common crystallization additives (GOL, CL) 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
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…
6OCH 2.0 Å, Crystal structure of VASH1-SVBP complex bound with parthenolide
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

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