7CB2 | pdb_00007cb2

The 6-phosphogluconate dehydrogenase (NADP-bound) from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb7CB2/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus str. Newman
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-10 Released: 2021-06-16
Deposition Author(s): Wang, H., Wang, M., Sun, H.
Funding Organization(s): The University Grants Committee, Research Grants Council (RGC), National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (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

The 6-phosphogluconate dehydrogenase (NADP-bound) structures from Staphylococcus aureus

Wang, H., Wang, M., Sun, H.

To be published.

Macromolecule Content

Total Structure Weight: 210.97 kDa
Atom Count: 14,777
Modeled Residue Count: 1,864
Deposited Residue Count: 1,872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase, decarboxylating	A, B, C, D	468	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 0 Gene Names: gnd, NWMN_1417 EC: 1.1.1.44
UniProt
Find proteins for A0A0H3KGN1 (Staphylococcus aureus (strain Newman)) Explore A0A0H3KGN1 Go to UniProtKB: A0A0H3KGN1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3KGN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], J [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	K [auth C], M [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain K [auth C] Focus chain M [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	F [auth A], G [auth A], I [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]