4I13 | pdb_00004i13

Nanobody ca1697 binding to the DHFR.folate binary complex

PDB DOI: https://doi.org/10.2210/pdb4I13/pdb

Classification: OXIDOREDUCTASE/IMMUNE SYSTEM
Organism(s): Escherichia coli K-12, Lama glama
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-19 Released: 2013-11-27
Deposition Author(s): Oyen, D., Steyaert, J., Barlow, J.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4I13

Ligand Structure Quality Assessment

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

Literature

Exploring an alternative antibody interaction mechanism

Oyen, D., Steyaert, J., Barlow, J.N.

To be published.

Macromolecule Content

Total Structure Weight: 33.29 kDa
Atom Count: 2,703
Modeled Residue Count: 287
Deposited Residue Count: 292
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	159	Escherichia coli K-12	Mutation(s): 0 Gene Names: folA, tmrA, b0048, JW0047 EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4 Go to UniProtKB: P0ABQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABQ4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ca1697 (nanobody)	B	133	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FOL Query on FOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FOLIC ACID C₁₉ H₁₉ N₇ O₆ OVBPIULPVIDEAO-LBPRGKRZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.180 (Depositor), 0.180 (DCC)
R-Value Work: 0.154 (Depositor), 0.155 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.76	α = 90
b = 58.05	β = 90
c = 114.38	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-11-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-27
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.