6EMJ | pdb_00006emj

FAB Fragment. AbVance: Increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery

PDB DOI: https://doi.org/10.2210/pdb6EMJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-10-02 Released: 2017-11-08
Deposition Author(s): Benz, J., Weigand, S., Dengl, S., Schlothauer, T., Auer, J., Ehler, A., Kettenberger, H., Lorenz, S., Hirschheydt, T., Georges, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.211 (Depositor), 0.214 (DCC)
R-Value Work:
0.165 (Depositor), 0.169 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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

Literature

AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery

Benz, J., Georges, G.

To be published.

Macromolecule Content

Total Structure Weight: 96.27 kDa
Atom Count: 6,915
Modeled Residue Count: 854
Deposited Residue Count: 882
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fAB heavy chain	A, C [auth H]	227	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
fAb light chain	B, D [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.211 (Depositor), 0.214 (DCC)
R-Value Work: 0.165 (Depositor), 0.169 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.48	α = 69.34
b = 73.869	β = 78.05
c = 76.92	γ = 70.2

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-11-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-08
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary