6LPG: Human VASH1-SVBP complex

human VASH1-SVBP complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 21 Oct 2020.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,358
Mol. weight: 37.53 kDa
Released: 21 Oct 2020

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

Secondary structure: helices and β-sheets

6LPG contains 16 α-helices and 8 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: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	69-70	2
α-helix	71-84	14
α-helix	88-95	8
α-helix	101-103	3
α-helix	105-110	6
α-helix	118-131	14
β-strand	134	1	1
α-helix	150-163	14
β-strand	167	1	1
α-helix	169-180	12
β-strand	186-197	12	2
β-strand	200-211	12	2
β-strand	214-218	5	2
α-helix	224-226	3
β-strand	229-233	5	2
α-helix	236-249	14
α-helix	252	1
β-strand	253-259	7	2
α-helix	260-264	5
α-helix	271-273	3
β-strand	278-281	4	2
α-helix	282-285	4
α-helix	288-302	15

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-51	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 1	A	protein	256	Homo sapiens	Q7L8A9 (AlphaFold model)
Small vasohibin-binding protein	B	protein	67	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6LPG_1 Tubulinyl-Tyr carboxypeptidase 1 (chains A)
GGVPFFVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPS
TPVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVIL
GIYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRT
LSELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELE
RHARDMRLKIGKGTGG

Sequence of entity 2 (B), FASTA

>6LPG_2 Small vasohibin-binding protein (chains B)
GDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQ
MQPPGEG

Primary citation

The crystal structure of the tetrameric human vasohibin-1-SVBP complex reveals a variable arm region within the structural core. Ikeda, A., Urata, S., Ando, T. et al. Acta Crystallogr D Struct Biol (2020) 76:993-1000. DOI 10.1107/S2059798320011298 · 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…
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
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 6LPG 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.