4HM0

Naphthalene 1,2-Dioxygenase bound to indole-3-acetate

PDB DOI: https://doi.org/10.2210/pdb4HM0/pdb

Classification: Oxidoreductase/Oxidoreductase inhibitor
Organism(s): Pseudomonas sp. C18
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-17 Released: 2013-10-30
Deposition Author(s): Ferraro, D.J., Ramaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.254
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Naphthalene 1,2-Dioxygenase bound to indole-3-acetate

Ferraro, D.J., Ramaswamy, S.

To be published.

Macromolecule Content

Total Structure Weight: 74.45 kDa
Atom Count: 5,655
Modelled Residue Count: 641
Deposited Residue Count: 643
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Naphthalene 1,2-dioxygenase subunit alpha	A	449	Pseudomonas sp. C18	Mutation(s): 0 Gene Names: doxB, NC_004999.1 EC: 1.14.12.12
UniProt
Find proteins for P0A111 (Pseudomonas sp. (strain C18)) Explore P0A111 Go to UniProtKB: P0A111
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A111
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Naphthalene 1,2-dioxygenase subunit beta	B	194	Pseudomonas sp. C18	Mutation(s): 0 Gene Names: doxD, NC_004999.1 EC: 1.14.12.12
UniProt
Find proteins for P0A113 (Pseudomonas sp. (strain C18)) Explore P0A113 Go to UniProtKB: P0A113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A113
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
IAC Query on IAC Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	1H-INDOL-3-YLACETIC ACID C₁₀ H₉ N O₂ SEOVTRFCIGRIMH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth B]	H [auth A], I [auth A], Q [auth A], S [auth B], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain Y [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	C [auth A] D [auth A] E [auth A] K [auth A] L [auth A] C [auth A], D [auth A], E [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], R [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]