7UI3

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

PDB DOI: https://doi.org/10.2210/pdb7UI3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-28 Released: 2024-02-21
Deposition Author(s): Yeh, S.-R., Geeraerts, Z.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free:
0.278 (Depositor), 0.280 (DCC)
R-Value Work:
0.244 (Depositor), 0.240 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

Yeh, S.-R., Geeraerts, Z.

To be published.

Macromolecule Content

Total Structure Weight: 181.6 kDa
Atom Count: 9,104
Modelled Residue Count: 1,207
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan 2,3-dioxygenase	A, B, C, D	380	Homo sapiens	Mutation(s): 0 Gene Names: TDO2, TDO EC: 1.13.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P48775 (Homo sapiens) Explore P48775 Go to UniProtKB: P48775
PHAROS: P48775 GTEx: ENSG00000151790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48775
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZIQ Query on ZIQ Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C], H [auth D]	alpha-methyl-L-tryptophan C₁₂ H₁₄ N₂ O₂ ZTTWHZHBPDYSQB-LBPRGKRZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.278 (Depositor), 0.280 (DCC)
R-Value Work: 0.244 (Depositor), 0.240 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.855	α = 90
b = 156.264	β = 90
c = 88.986	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Coot	model building
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Yeh, S.-R.

Geeraerts, Z.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115773
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM126297

Revision History (Full details and data files)

Version 1.0: 2024-02-21
Type: Initial release

Prepare Data

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Deposit Data

Help and Resources

7UI3

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)