6M34

Structural and functional insights into an Archaeal synthase

PDB DOI: https://doi.org/10.2210/pdb6M34/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli ATCC 8739
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2020-03-02 Released: 2021-02-03
Deposition Author(s): Wei, C., Sixue, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.269
R-Value Work: 0.247
R-Value Observed: 0.248

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and mechanistic insights into the biosynthesis of Digeranylgeranylglyceryl phosphate synthase in membranes

Wei, C., Sixue, R.

To be published.

Macromolecule Content

Total Structure Weight: 65.93 kDa
Atom Count: 4,603
Modelled Residue Count: 560
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Digeranylgeranylglyceryl phosphate synthase	A, B	283	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: MJ0279 EC: 2.5.1.42 Membrane Entity: Yes
UniProt
Find proteins for Q57727 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57727 Go to UniProtKB: Q57727
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57727
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPG (Subject of Investigation/LOI) Query on MPG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B]	C [auth A], F [auth A], I [auth B], K [auth B]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B]
DMA (Subject of Investigation/LOI) Query on DMA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	DIMETHYLALLYL DIPHOSPHATE C₅ H₁₂ O₇ P₂ CBIDRCWHNCKSTO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
LDA (Subject of Investigation/LOI) Query on LDA Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]