7CN3 | pdb_00007cn3

2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid

PDB DOI: https://doi.org/10.2210/pdb7CN3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-30 Released: 2020-12-16
Deposition Author(s): Liu, G.Q., Tang, H.Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.238 (Depositor), 0.241 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (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

2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid

Liu, G.Q., Tang, H.Z.

(2020) Nat Commun

Macromolecule Content

Total Structure Weight: 245.4 kDa
Atom Count: 17,618
Modeled Residue Count: 2,090
Deposited Residue Count: 2,178
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-dihydroxypyridine 5,6-dioxygenase	A, B, C, D, E A, B, C, D, E, F	363	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: nicX, PP_3945 EC: 1.13.11.9
UniProt
Find proteins for Q88FY1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88FY1 Go to UniProtKB: Q88FY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88FY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C]	P [auth C], T [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain P [auth C] Focus chain T [auth D]
D6O (Subject of Investigation/LOI) Query on D6O Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B]	(~{Z})-4-formamido-4-oxidanylidene-but-2-enoic acid C₅ H₅ N O₄ HSKSAKBZUITULZ-UPHRSURJSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
G6C (Subject of Investigation/LOI) Query on G6C Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain V [auth E] SDF format, chain R [auth D] SDF format, chain M [auth C] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth E] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth E] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C]	M [auth C], R [auth D], V [auth E], Z [auth F]	5-oxidanyl-1H-pyridin-2-one C₅ H₅ N O₂ CHGPEDOMXOLANF-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain M [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Z [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain I [auth A] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] I [auth A] N [auth C] O [auth C] AA [auth F], BA [auth F], I [auth A], N [auth C], O [auth C], S [auth D], W [auth E], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain I [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain I [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain X [auth E]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain U [auth E] SDF format, chain Q [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] L [auth C] Q [auth D] U [auth E] G [auth A], J [auth B], L [auth C], Q [auth D], U [auth E], Y [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain Y [auth F]