2P80 | pdb_00002p80

Solution structure of the complex between nitrite reductase and pseudoazurin from A. faecalis

PDB DOI: https://doi.org/10.2210/pdb2P80/pdb
BMRB: 6043

Classification: OXIDOREDUCTASE
Organism(s): Alcaligenes faecalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-03-21 Released: 2007-12-11
Deposition Author(s): Vlasie, M.D., Ubbink, M.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 134
Conformers Submitted: 20
Selection Criteria: structures closest to the average

wwPDB Validation 3D Report Full Report

Validation slider image for 2P80

This is version 1.3 of the entry. See complete history.

Literature

Low resolution solution structure of the 152 kDa complex between nitrite reductase and pseudoazurin from A. faecalis by paramagnetic NMR.

Vlasie, M.D., Fernandez-Busnadiego, R., Prudencio, M., Ubbink, M.

To be published.

Macromolecule Content

Total Structure Weight: 125.88 kDa
Atom Count: 8,628
Modeled Residue Count: 1,130
Deposited Residue Count: 1,146
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	341	Alcaligenes faecalis	Mutation(s): 0 Gene Names: nirK, nir EC: 1.7.2.1
UniProt
Find proteins for P38501 (Alcaligenes faecalis) Explore P38501 Go to UniProtKB: P38501
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38501
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudoazurin	D	123	Alcaligenes faecalis	Mutation(s): 0
UniProt
Find proteins for P04377 (Alcaligenes faecalis) Explore P04377 Go to UniProtKB: P04377
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04377
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GD Query on GD Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] J [auth B] K [auth B] O [auth C] E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], T [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 134
Conformers Submitted: 20
Selection Criteria: structures closest to the average

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2022-03-16
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-05-22
Changes: Data collection

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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.