8H7I

Structure of nanobody 11A in complex with quinalphos

PDB DOI: https://doi.org/10.2210/pdb8H7I/pdb

Classification: IMMUNE SYSTEM
Organism(s): Camelus bactrianus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-20 Released: 2023-10-25
Deposition Author(s): Wang, H., Li, J.D., Shen, X., Xu, Z.L., Sun, Y.M.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of nanobody 11A in complex with quinalphos

Jiadong, L., Hong, W.

To be published.

Macromolecule Content

Total Structure Weight: 30.98 kDa
Atom Count: 1,911
Modelled Residue Count: 234
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 11A	A, B	140	Camelus bactrianus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WYN (Subject of Investigation/LOI) Query on WYN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	quinalphos C₁₂ H₁₅ N₂ O₃ P S JYQUHIFYBATCCY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.113	α = 90
b = 96.123	β = 90
c = 91.121	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFE0116600

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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.