9L29 | pdb_00009l29

YdiU in complex with NAD, short soaking experiment

PDB DOI: https://doi.org/10.2210/pdb9L29/pdb

Classification: LYASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-16 Released: 2026-01-14
Deposition Author(s): Liu, K., Zhang, T., Wang, T., Xiang, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.242 (Depositor), 0.249 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Hydrolyzing NAD to NMN and ADP by SelO required for Mitochondria Homeostasis

Jia, X., Zhang, T., Yang, C., Liu, K., Wu, L., Diao, L., Yang, Y., Wu, J., Li, Y., Sun, W., Zhang, K., Jiang, Y., Zhao, Y., Zhang, X., Jiang, P., Jiang, Y., Yu, Q., Xiang, S., Fu, Y., Wang, T.

(2026) Cell

Macromolecule Content

Total Structure Weight: 56.76 kDa
Atom Count: 4,066
Modeled Residue Count: 477
Deposited Residue Count: 491
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein adenylyltransferase SelO	A	491	Escherichia coli	Mutation(s): 0 Gene Names: selO, BKL28_004258, HLZ39_02825 EC: 2.7.7.108 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for A0A2T1ME41 (Escherichia coli) Explore A0A2T1ME41 Go to UniProtKB: A0A2T1ME41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2T1ME41
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.242 (Depositor), 0.249 (DCC)
R-Value Work: 0.199 (Depositor), 0.207 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.56	α = 90
b = 95.34	β = 90
c = 118.95	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82350116

Revision History (Full details and data files)

Version 1.0: 2026-01-14
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.