8STL | pdb_00008stl

Crystal Structure of Nanobody PIK3_Nb16 against wild-type PI3Kalpha

PDB DOI: https://doi.org/10.2210/pdb8STL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-10 Released: 2024-05-22
Deposition Author(s): Nwafor, J.N., Srinivasan, L., Chen, Z., Gabelli, S.B., Iheanacho, A., Alzogaray, V., Klinke, S.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.255 (Depositor), 0.256 (DCC)
R-Value Work:
0.189 (Depositor), 0.198 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Development of isoform specific nanobodies for Class I PI3Ks

Nwafor, J.N., Srinivasan, L., Chen, Z., Gabelli, S.B.

To be published.

Macromolecule Content

Total Structure Weight: 63.21 kDa
Atom Count: 4,307
Modeled Residue Count: 491
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody PIK3_Nb16	A [auth C], B, C [auth A], D	141	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain J [auth B]	E [auth C] F [auth C] G [auth B] H [auth B] I [auth B] E [auth C], F [auth C], G [auth B], H [auth B], I [auth B], J [auth B], K [auth A], L [auth A], M [auth A], N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.255 (Depositor), 0.256 (DCC)
R-Value Work: 0.189 (Depositor), 0.198 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.607	α = 90
b = 59.383	β = 111.06
c = 70.702	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.