2GF3

Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution.

PDB DOI: https://doi.org/10.2210/pdb2GF3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus sp. (in: firmicutes)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-03-21 Released: 2007-02-06
Deposition Author(s): Chen, Z., Trickey, P., Jorns, M.S., Mathews, F.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.195
R-Value Work: 0.170

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution.

Chen, Z., Trickey, P., Jorns, M.S., Mathews, F.S.

To be published.

Macromolecule Content

Total Structure Weight: 88.76 kDa
Atom Count: 7,300
Modelled Residue Count: 770
Deposited Residue Count: 778
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monomeric sarcosine oxidase	A, B	389	Bacillus sp. (in: firmicutes)	Mutation(s): 0 Gene Names: soxA, sox EC: 1.5.3.1
UniProt
Find proteins for P40859 (Bacillus sp. (strain B-0618)) Explore P40859 Go to UniProtKB: P40859
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40859
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
FOA Query on FOA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B]	F [auth A], G [auth A], L [auth B], N [auth B]	2-FUROIC ACID C₅ H₄ O₃ SMNDYUVBFMFKNZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], J [auth B], K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	H [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.195
R-Value Work: 0.170
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.727	α = 90
b = 69.44	β = 94.16
c = 73.671	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2012-03-28
Changes: Non-polymer description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-16
Changes: Structure summary