9W5W | pdb_00009w5w

Crystal structure of Namat in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb9W5W/pdb

Classification: VIRAL PROTEIN
Organism(s): Bacillus phage SPbetaL1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-02 Released: 2025-12-24
Deposition Author(s): Bao, H., Xu, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Namat in complex with NAD

Bao, H., Xu, L.

To be published.

Macromolecule Content

Total Structure Weight: 227.98 kDa
Atom Count: 16,631
Modeled Residue Count: 1,930
Deposited Residue Count: 1,984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide phosphoribosyltransferase	A, B, C, D	496	Bacillus phage SPbetaL1	Mutation(s): 0 EC: 2.4.2.12
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
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], I [auth B], K [auth C], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]