6K81

Crystal structure of human VASH1-SVBP complex

PDB DOI: https://doi.org/10.2210/pdb6K81/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-11 Released: 2020-02-19
Deposition Author(s): Liu, X., Wang, H., Zhang, Y., Feng, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.242
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into tubulin detyrosination by vasohibins-SVBP complex.

Liu, X., Wang, H., Zhu, J., Xie, Y., Liang, X., Chen, Z., Feng, Y., Zhang, Y.

(2019) Cell Discov 5: 65-65

PubMed: 31908845 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-019-0133-7
Primary Citation of Related Structures:
6K81

Organizational Affiliation

1Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029 China.

Macromolecule Content

Total Structure Weight: 48.85 kDa
Atom Count: 2,316
Modelled Residue Count: 274
Deposited Residue Count: 431
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulinyl-Tyr carboxypeptidase 1	A	365	Homo sapiens	Mutation(s): 0 Gene Names: VASH1, KIAA1036, VASH EC: 3.4.17.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L8A9 (Homo sapiens) Explore Q7L8A9 Go to UniProtKB: Q7L8A9
PHAROS: Q7L8A9 GTEx: ENSG00000071246
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7L8A9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small vasohibin-binding protein	B	66	Homo sapiens	Mutation(s): 0 Gene Names: SVBP, CCDC23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N300 (Homo sapiens) Explore Q8N300 Go to UniProtKB: Q8N300
PHAROS: Q8N300 GTEx: ENSG00000177868
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N300
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.242
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.452	α = 90
b = 128.995	β = 90
c = 44.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31822012

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.