5MO3 | pdb_00005mo3

Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 8.5

PDB DOI: https://doi.org/10.2210/pdb5MO3/pdb

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

Deposited: 2016-12-13 Released: 2018-05-02
Deposition Author(s): Skrabana, R., Novak, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.192 (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

Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 8.5

Skrabana, R., Novak, M.

To be published.

Macromolecule Content

Total Structure Weight: 50.39 kDa
Atom Count: 3,922
Modelled Residue Count: 446
Deposited Residue Count: 453
Unique protein chains: 3

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated protein tau	A	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens) Explore P10636 Go to UniProtKB: P10636
PHAROS: P10636 GTEx: ENSG00000186868
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10636
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of monoclonal antibody, heavy chain	B [auth H]	221	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of monoclonal antibody, light chain	C [auth L]	218	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	D [auth B]	2		N/A	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth L] SDF format, chain H [auth L] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L]	E [auth H], F [auth H], G [auth L], H [auth L]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L] Focus chain H [auth L] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L] Focus chain H [auth L]

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	D [auth B]	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.728	α = 90
b = 60.128	β = 109.25
c = 69.315	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):

Skrabana, R.

Novak, M.

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 2.0: 2020-03-11
Changes: 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