6D9Y | pdb_00006d9y

Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum with partially occupied NAD

PDB DOI: https://doi.org/10.2210/pdb6D9Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paraburkholderia phymatum STM815
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-30 Released: 2018-06-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.152 (Depositor), 0.160 (DCC)
R-Value Work:
0.143 (Depositor)
R-Value Observed:
0.143 (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

Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum with partially occupied NAD

Mayclin, S.J., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 56.53 kDa
Atom Count: 4,726
Modeled Residue Count: 502
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	258	Paraburkholderia phymatum STM815	Mutation(s): 0 Gene Names: Bphy_3470 EC: 1.3.8
UniProt
Find proteins for B2JLJ0 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JLJ0 Go to UniProtKB: B2JLJ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2JLJ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
OXM Query on OXM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B]	E [auth A], H [auth B], J [auth B]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	F [auth A], G [auth A], K [auth B], L [auth B], M [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]