4TPR | pdb_00004tpr

Structure of Tau5 antibody Fab fragment

PDB DOI: https://doi.org/10.2210/pdb4TPR/pdb

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

Deposited: 2014-06-09 Released: 2015-07-29
Deposition Author(s): Cehlar, O., Skrabana, R., Novak, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.143 (Depositor), 0.156 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of Tau5 antibody Fab fragment

Cehlar, O., Skrabana, R., Novak, M.

To be published.

Macromolecule Content

Total Structure Weight: 49.87 kDa
Atom Count: 4,025
Modeled Residue Count: 439
Deposited Residue Count: 439
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
If kappa light chain	A [auth L]	218	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3 Go to UniProtKB: A2NHM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2NHM3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B [auth H]	221	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
33O Query on 33O Download:Ideal Coordinates CCD File SDF format, chain Q [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain Q [auth H]	Q [auth H]	3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol C₂₆ H₅₄ O₁₄ AKWFJQNBHYVIPY-UHFFFAOYSA-N		Interactions Focus chain Q [auth H] Interactions & Density Focus chain Q [auth H]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth L] SDF format, chain D [auth L] MOL2 format, chain C [auth L] MOL2 format, chain D [auth L] mmCIF format, chain C [auth L] mmCIF format, chain D [auth L]	C [auth L], D [auth L]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain D [auth L] Interactions & Density Focus chain C [auth L] Focus chain D [auth L]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L] mmCIF format, chain G [auth L]	G [auth L]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain R [auth H] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain R [auth H] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain L mmCIF format, chain R [auth H]	I [auth L], J [auth L], K [auth L], L, R [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain R [auth H] Interactions & Density Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain R [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain E [auth L]	E [auth L], F [auth L], N [auth H], O [auth H], P [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth L] MOL2 format, chain H [auth L] mmCIF format, chain H [auth L]	H [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Interactions & Density Focus chain H [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.191 (Depositor), 0.200 (DCC)
R-Value Work: 0.143 (Depositor), 0.156 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.374	α = 90
b = 50.408	β = 115.35
c = 75.169	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Cehlar, O.

Skrabana, R.

Novak, M.

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary