8H7R

Structure of nanobody 11A in complex with coumaphos

PDB DOI: https://doi.org/10.2210/pdb8H7R/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: 2.00 Å
R-Value Free: 0.261
R-Value Work: 0.224
R-Value Observed: 0.226

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 coumaphos

Jiadong, L., Hong, W.

To be published.

Macromolecule Content

Total Structure Weight: 15.55 kDa
Atom Count: 952
Modelled Residue Count: 118
Deposited Residue Count: 140
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 11A	A	140	Camelus bactrianus	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
WZ0 (Subject of Investigation/LOI) Query on WZ0 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	coumaphos C₁₄ H₁₆ Cl O₅ P S BXNANOICGRISHX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.261
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.166	α = 90
b = 84.166	β = 90
c = 32.301	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
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: 2024-10-23
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.