5MHE

Crystal structure of anti-T4 Fab fragment with T4

PDB DOI: https://doi.org/10.2210/pdb5MHE/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-24 Released: 2018-08-08
Deposition Author(s): Parkkinen, T., Rouvinen, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.227
R-Value Work: 0.178
R-Value Observed: 0.181

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structures of anti-T4 Fab fragment

Parkkinen, T., Rouvinen, J.

To be published.

Macromolecule Content

Total Structure Weight: 49.75 kDa
Atom Count: 3,673
Modelled Residue Count: 432
Deposited Residue Count: 448
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-fragment	A [auth L]	213	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-fragment	B [auth H]	235	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T44 Query on T44 Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	3,5,3',5'-TETRAIODO-L-THYRONINE C₁₅ H₁₁ I₄ N O₄ XUIIKFGFIJCVMT-LBPRGKRZSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L] mmCIF format, chain C [auth L]	C [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth L] Interactions & Density Focus chain C [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H]	E [auth H], F [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.227
R-Value Work: 0.178
R-Value Observed: 0.181
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 131.73	α = 90
b = 55.33	β = 97.77
c = 61.16	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Parkkinen, T.

Rouvinen, J.

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references
Version 2.1: 2024-01-17
Changes: Refinement description

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5MHE

Crystal structure of anti-T4 Fab fragment with T4

Crystal structures of anti-T4 Fab fragment

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2