9H5X | pdb_00009h5x

Crystal structure of human V122I transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone compound

PDB DOI: https://doi.org/10.2210/pdb9H5X/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-10-23 Released: 2025-11-05
Deposition Author(s): Varejao, N., Pinheiro, F., Pallares, I., Ventura, S., Reverter, D.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.222 (Depositor), 0.225 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human V122I transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone compound

Varejao, N., Pinheiro, F., Pallares, I., Ventura, S., Reverter, D.

To be published.

Macromolecule Content

Total Structure Weight: 27.65 kDa
Atom Count: 2,000
Modeled Residue Count: 232
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	125	Homo sapiens	Mutation(s): 1 Gene Names: TTR, PALB
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AQI (Subject of Investigation/LOI) Query on AQI Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(3-fluoranyl-5-oxidanyl-phenyl)-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone C₁₃ H₈ F N O₆ UHVIBVZISWKHAF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.222 (Depositor), 0.225 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.708	α = 90
b = 65.496	β = 90
c = 83.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2021-124602OB-I00

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.