7SNW | pdb_00007snw

1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576

PDB DOI: https://doi.org/10.2210/pdb7SNW/pdb

Classification: OXIDOREDUCTASE/INHIBITOR
Organism(s): Oplophorus gracilirostris
Expression System: Escherichia coli KRX
Mutation(s): Yes

Deposited: 2021-10-28 Released: 2022-11-16
Deposition Author(s): Lovell, S., Mehzabeen, N., Battaile, K.P., Wood, M.G., Encell, L.P., Wood, K.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.175 (Depositor), 0.180 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576

Encell, L.P., Lovell, S., Mehzabeen, N., Battaile, K.P., Wood, M.G., Wood, K.V.

To be published.

Macromolecule Content

Total Structure Weight: 60.65 kDa
Atom Count: 4,732
Modeled Residue Count: 510
Deposited Residue Count: 522
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oplophorus-luciferin 2-monooxygenase catalytic subunit	A, B, C	174	Oplophorus gracilirostris	Mutation(s): 16 EC: 1.13.12.13
UniProt
Find proteins for Q9GV45 (Oplophorus gracilirostris) Explore Q9GV45 Go to UniProtKB: Q9GV45
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GV45
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9Y4 (Subject of Investigation/LOI) Query on 9Y4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	I [auth A], P [auth B], W [auth C]	N-[(4-methylphenyl)methyl]-N~2~-phenylglycinamide C₁₆ H₁₈ N₂ O VRFYXFGMPCGHJQ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C]
9YR (Subject of Investigation/LOI) Query on 9YR Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	H [auth A], O [auth B], V [auth C]	2-(methoxycarbonyl)thiophene-3-sulfonic acid C₆ H₆ O₅ S₂ AYKJLZKNHNYZON-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C]	E [auth A], F [auth A], G [auth A], N [auth B], U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain U [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	J [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B]	K [auth A], L [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C]	D [auth A], M [auth B], T [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth B] Focus chain T [auth C]