7XLF | pdb_00007xlf

Crystal structure of CH3-THF complex of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6

PDB DOI: https://doi.org/10.2210/pdb7XLF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sphingobium sp. SYK-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-21 Released: 2023-04-26
Deposition Author(s): Yu, H.Y., Senda, M., Senda, T.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (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 structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6

Yu, H.Y., Senda, T.

To be published.

Macromolecule Content

Total Structure Weight: 65.53 kDa
Atom Count: 4,777
Modeled Residue Count: 565
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methylenetetrahydrofolate reductase	A, B	288	Sphingobium sp. SYK-6	Mutation(s): 0 Gene Names: metF, SLG_12750 EC: 1.5.1.20 (PDB Primary Data), 1.5.1.54 (UniProt)
UniProt
Find proteins for G2IQS8 (Sphingobium sp. (strain NBRC 103272 / SYK-6)) Explore G2IQS8 Go to UniProtKB: G2IQS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G2IQS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
C2F (Subject of Investigation/LOI) Query on C2F Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID C₂₀ H₂₅ N₇ O₆ ZNOVTXRBGFNYRX-STQMWFEESA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]