3BD3

Crystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals

PDB DOI: https://doi.org/10.2210/pdb3BD3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-14 Released: 2008-04-01
Deposition Author(s): Park, S.K., Kim, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.270
R-Value Work: 0.229
R-Value Observed: 0.229

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals

Park, S.Y., Lee, W.R., Lee, S.C., Kwon, M.H., Kim, Y.S., Kim, J.S.

(2008) Proteins 71: 2091-2096

PubMed: 18338383 Search on PubMed
DOI: https://doi.org/10.1002/prot.22011
Primary Citation of Related Structures:
3BD3, 3BD4, 3BD5

Organizational Affiliation

Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Korea.

Macromolecule Content

Total Structure Weight: 25.13 kDa
Atom Count: 1,982
Modelled Residue Count: 224
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
catalytic antibody	A, B	112	Mus musculus	Mutation(s): 0 Gene Names: 3d8 vl
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
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.270
R-Value Work: 0.229
R-Value Observed: 0.229
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.746	α = 90
b = 61.746	β = 90
c = 95.752	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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 R01GM133198.