4BE9

Open conformation of O. piceae sterol esterase

PDB DOI: https://doi.org/10.2210/pdb4BE9/pdb

Classification: HYDROLASE
Organism(s): Ophiostoma piceae
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2013-03-06 Released: 2014-03-26
Deposition Author(s): Gutierrez-Fernandez, J., Vaquero, M.E., Prieto, A., Barriuso, J., Gonzalez, M.J., Hermoso, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 121.67 kDa
Atom Count: 9,295
Modelled Residue Count: 1,075
Deposited Residue Count: 1,090
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROL ESTERASE	A, B	545	Ophiostoma piceae	Mutation(s): 0 EC: 3.1.1.13
UniProt
Find proteins for Q2TFW1 (Ophiostoma piceae) Explore Q2TFW1 Go to UniProtKB: Q2TFW1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2TFW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7P9 Query on 7P9 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B]	E [auth A], N [auth B]	[(2R)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate C₁₉ H₃₇ O₈ P XKPYMIOWFWFMRM-QGZVFWFLSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B]	C [auth A], D [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	G [auth A], K [auth A], S [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth A] Focus chain S [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	H [auth A] L [auth A] O [auth B] P [auth B] Q [auth B] H [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	I [auth A], T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B]	J [auth A], V [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.206
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.123	α = 90
b = 164.123	β = 90
c = 93.994	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Gutierrez-Fernandez, J.

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2014-09-24
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary