1VE6

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1

PDB DOI: https://doi.org/10.2210/pdb1VE6/pdb

Classification: HYDROLASE
Organism(s): Aeropyrum pernix
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-03-27 Released: 2004-11-02
Deposition Author(s): Bartlam, M., Wang, G., Gao, R., Yang, H., Zhao, X., Xie, G., Cao, S., Feng, Y., Rao, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229
R-Value Work: 0.193
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 126.99 kDa
Atom Count: 9,349
Modelled Residue Count: 1,148
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylamino-acid-releasing enzyme	A, B	582	Aeropyrum pernix	Mutation(s): 0 EC: 3.4.19.1
UniProt
Find proteins for Q9YBQ2 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YBQ2 Go to UniProtKB: Q9YBQ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9YBQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229
R-Value Work: 0.193
R-Value Observed: 0.207
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.73	α = 90
b = 104.739	β = 90
c = 170.944	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-11-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-11-02
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Structure summary

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Deposit Data

Help and Resources

1VE6

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)