5BXO | pdb_00005bxo

Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n2m3

PDB DOI: https://doi.org/10.2210/pdb5BXO/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-06-09 Released: 2016-06-29
Deposition Author(s): Xu, W., Fischer, G., Hyvonen, M., Itzhaki, L.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free:
0.203 (Depositor), 0.205 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human Tankyrase-2 in Complex with Extended Stapled Peptide sp4n2m3

Xu, W., Lau, Y.H., Fischer, G., Chattopadhyay, A., Tan, Y.S., Verma, C., Hyvonen, M., Spring, D.S., Itzhaki, L.S.

To be published.

Macromolecule Content

Total Structure Weight: 38.35 kDa
Atom Count: 3,203
Modeled Residue Count: 343
Deposited Residue Count: 348
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-2	A, B	164	Homo sapiens	Mutation(s): 0 Gene Names: TNKS2, PARP5B, TANK2, TNKL EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens) Explore Q9H2K2 Go to UniProtKB: Q9H2K2
PHAROS: Q9H2K2 GTEx: ENSG00000107854
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H2K2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-2	C, D	10	Homo sapiens	Mutation(s): 0 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens) Explore Q9H2K2 Go to UniProtKB: Q9H2K2
PHAROS: Q9H2K2 GTEx: ENSG00000107854
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H2K2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4XP Query on 4XP Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C]	N [auth C], O [auth D]	4,4'-propane-1,3-diylbis(1-methyl-1H-1,2,3-triazole) C₉ H₁₄ N₆ NXBVOKRBXODKCH-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain O [auth D] Interactions & Density Focus chain N [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	H [auth A], L [auth B], M [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.203 (Depositor), 0.205 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.823	α = 78.45
b = 46.014	β = 88.99
c = 54.472	γ = 72.35

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
Coot	model building
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G1002329

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2017-09-13
Changes: Advisory, Author supporting evidence
Version 1.2: 2024-10-23
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary

5BXO | pdb_00005bxo

Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n2m3

Literature

Human Tankyrase-2 in Complex with Extended Stapled Peptide sp4n2m3

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2