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), 0.260 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 J [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] 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 J [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] 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 J [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]	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]