2WQA | pdb_00002wqa

Complex of TTR and RBP4 and Oleic Acid

PDB DOI: https://doi.org/10.2210/pdb2WQA/pdb

Classification: HYDROLASE/SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2009-08-14 Released: 2010-09-01
Deposition Author(s): Nanao, M., Mercer, D., Nguyen, L., Buckley, D., Stout, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Rbp4 Bound to Linoleic Acid and Ttr

Nanao, M., Stout, T.J.

To be published.

Macromolecule Content

Total Structure Weight: 97.87 kDa
Atom Count: 6,597
Modeled Residue Count: 821
Deposited Residue Count: 870
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSTHYRETIN	A, B, C, D	129	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens) Explore P02766 Go to UniProtKB: P02766
PHAROS: P02766 GTEx: ENSG00000118271
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02766
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINOL-BINDING PROTEIN 4	E, F	177	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02753 (Homo sapiens) Explore P02753 Go to UniProtKB: P02753
PHAROS: P02753 GTEx: ENSG00000138207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02753
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain O [auth F] MOL2 format, chain K [auth E] MOL2 format, chain O [auth F] mmCIF format, chain K [auth E] mmCIF format, chain O [auth F]	K [auth E], O [auth F]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain K [auth E] Focus chain O [auth F] Interactions & Density Focus chain K [auth E] Focus chain O [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain L [auth E] mmCIF format, chain M [auth E] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F]	G [auth A] H [auth A] I [auth C] J [auth C] L [auth E] G [auth A], H [auth A], I [auth C], J [auth C], L [auth E], M [auth E], N [auth E], P [auth F], Q [auth F], R [auth F], S [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.662	α = 90
b = 138.662	β = 90
c = 122.789	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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: 2010-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-06-02
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-04-03
Changes: Data collection, Other, Source and taxonomy
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary

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Complex of TTR and RBP4 and Oleic Acid

Crystal Structure of Rbp4 Bound to Linoleic Acid and Ttr

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2