6QTL | pdb_00006qtl

Caffeine recognizing nanobody

PDB DOI: https://doi.org/10.2210/pdb6QTL/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Camelidae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-02-25 Released: 2019-04-10
Deposition Author(s): Lesne, J., Guichou, J.F., Labesse, G., Cohen-Gonsaud, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.259 (Depositor), 0.261 (DCC)
R-Value Work:
0.194 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural basis for chemically-induced homodimerization of a single domain antibody

Lesne, J.x.

To be published.

Macromolecule Content

Total Structure Weight: 105.31 kDa
Atom Count: 7,949
Modeled Residue Count: 948
Deposited Residue Count: 956
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH	A [auth H], B [auth A], E [auth D], F [auth E]	119	Camelidae	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH	C [auth B], D [auth C], G [auth F], H [auth G]	120	Camelidae	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFF Query on CFF Download:Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain J [auth A] SDF format, chain K [auth D] SDF format, chain L [auth E] MOL2 format, chain I [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] mmCIF format, chain I [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E]	I [auth H], J [auth A], K [auth D], L [auth E]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth A] Focus chain K [auth D] Focus chain L [auth E] Interactions & Density Focus chain I [auth H] Focus chain J [auth A] Focus chain K [auth D] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.259 (Depositor), 0.261 (DCC)
R-Value Work: 0.194 (Depositor), 0.199 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.26	α = 90
b = 60.99	β = 93.69
c = 87.67	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Cohen-Gonsaud, M.

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.