6A1E | pdb_00006a1e

Crystal structure of a synthase 1 from Santalum album in complex with ligand fps

PDB DOI: https://doi.org/10.2210/pdb6A1E/pdb

Classification: TRANSFERASE
Organism(s): Santalum album
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-07 Released: 2019-06-12
Deposition Author(s): Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.199 (Depositor), 0.210 (DCC)
R-Value Work:
0.154 (Depositor), 0.170 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of a synthase 1 from Santalum album in complex with ligand

Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 66.54 kDa
Atom Count: 4,678
Modelled Residue Count: 512
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sesquisabinene B synthase 1	A	566	Santalum album	Mutation(s): 0
UniProt
Find proteins for A0A0A0RDR2 (Santalum album) Explore A0A0A0RDR2 Go to UniProtKB: A0A0A0RDR2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A0RDR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FPS (Subject of Investigation/LOI) Query on FPS Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE C₁₅ H₂₈ O₆ P₂ S MYMLCRQRXFRQGP-YFVJMOTDSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.199 (Depositor), 0.210 (DCC)
R-Value Work: 0.154 (Depositor), 0.170 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.611	α = 90
b = 139.498	β = 90
c = 110.962	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 2.0: 2020-09-02
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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Crystal structure of a synthase 1 from Santalum album in complex with ligand fps

Crystal structure of a synthase 1 from Santalum album in complex with ligand

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations