6ELE | pdb_00006ele

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/pdb6ELE/pdb

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

Deposited: 2017-09-28 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: 1.78 Å
R-Value Free:
0.218 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

This is version 1.3 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: 96.33 kDa
Atom Count: 6,964
Modeled Residue Count: 853
Deposited Residue Count: 882
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.218 (Depositor), 0.230 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.417	α = 101.93
b = 74.131	β = 102.23
c = 76.515	γ = 111.27

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SADABS	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: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary