6J4P: Tubulinyl-Tyr carboxypeptidase 2

Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications. Determined by X-ray diffraction at 1.6 Å resolution. Released 1 May 2019.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,891
Mol. weight: 37.47 kDa
Ligands: BJL
Released: 1 May 2019

Explore 6J4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J4P contains 14 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: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	1
α-helix	58-59	2
α-helix	60-73	14
α-helix	77-85	9
α-helix	96-99	4
α-helix	107-121	15
β-strand	123	1	2
β-strand	128-129	2	1
β-strand	138	1	3
α-helix	139-152	14
β-strand	156	1	2
α-helix	158-169	12
β-strand	176-186	11	4
β-strand	189-200	12	4
β-strand	203-207	5	4
α-helix	213-215	3
β-strand	218-222	5	4
α-helix	225-238	14
β-strand	242-248	7	4
α-helix	250-253	4
β-strand	261	1	3
α-helix	262-263	2
β-strand	267-270	4	4
α-helix	276-292	17

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	27-59	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 2	A	protein	251	Homo sapiens	Q86V25 (AlphaFold model)
Small vasohibin-binding protein	B	protein	66	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J4P_1 Tubulinyl-Tyr carboxypeptidase 2 (chains A)
GVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSM
TIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILG
IYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTL
SDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEK
YARDMRMKILK

Sequence of entity 2 (B), FASTA

>6J4P_2 Small vasohibin-binding protein (chains B)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQ
MQPPGE

Ligands and cofactors

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

Primary citation

Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex. Wang, N., Bosc, C., Ryul Choi, S. et al. Nat Struct Mol Biol (2019) 26:571-582. DOI 10.1038/s41594-019-0241-y · PubMed

Other PDB entries of the same protein (UniProt Q86V25 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QBY 2.09 Å, Crystal structure of VASH 2 in complex with SVBP
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J4O 2.3 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J4Q 2.7 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J4S 2.8 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
7ZCW 3.6 Å, Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP

Browse structure collections

About this viewer

MolViewer shows 6J4P 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.