5MTH | pdb_00005mth

Structure of DC8E8 Fab at pH 6.5 crystallized in spacegroup P21

PDB DOI: https://doi.org/10.2210/pdb5MTH/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2017-01-09 Released: 2018-05-02
Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.235 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.170 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Literature

Structure of DC8E8 Fab at pH 6.5 crystallized in spacegroup P21

Skrabana, R.

To be published.

Macromolecule Content

Total Structure Weight: 97.82 kDa
Atom Count: 7,524
Modeled Residue Count: 879
Deposited Residue Count: 880
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab heavy chain	A [auth H], C [auth A]	221	Mus musculus	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
antibody Fab light chain	B [auth L], D [auth B]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	E [auth C], F [auth D], G [auth E], H [auth F]	2		N/A	Interactions Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Interactions & Density Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth H] SDF format, chain I [auth H] MOL2 format, chain M [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth H] MOL2 format, chain I [auth H] mmCIF format, chain M [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth H] mmCIF format, chain I [auth H]	I [auth H], J [auth H], K [auth A], L [auth A], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A [auth H], C [auth A]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	E [auth C], F [auth D], G [auth E], H [auth F]	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F] Interactions & Density Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth E] Focus chain H [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.235 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.170 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.45	α = 90
b = 111.77	β = 90.56
c = 95.64	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2019-08-14
Changes: Data collection
Version 2.0: 2020-03-11
Changes: Atomic model, Data collection, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 3.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.2: 2024-11-06
Changes: Structure summary