2WK2 | pdb_00002wk2

Chitinase A from Serratia marcescens ATCC990 in complex with Chitotrio-thiazoline dithioamide.

PDB DOI: https://doi.org/10.2210/pdb2WK2/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Mutation(s): No

Deposited: 2009-06-04 Released: 2010-03-16
Deposition Author(s): Taylor, E.J., Dennis, R.J., Macdonald, J.M., Tarling, C.A., Knapp, S., Withers, S.G., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.215 (Depositor), 0.199 (DCC)
R-Value Work:
0.165 (Depositor)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Chitinase Inhibition by Chitobiose and Chitotriose Thiazolines.

Macdonald, J.M., Tarling, C.A., Taylor, E.J., Dennis, R.J., Myers, D.S., Knapp, S., Davies, G.J., Withers, S.G.

(2010) Angew Chem Int Ed Engl 49: 2599

PubMed: 20209544 Search on PubMed
DOI: https://doi.org/10.1002/anie.200906644
Primary Citation Related Structures:
2WK2, 2WLY, 2WLZ, 2WM0

Organizational Affiliation

Department of Chemistry, University of British Columbia, Vancouver, V6T1Z3 Canada.

Macromolecule Content

Total Structure Weight: 60.14 kDa
Atom Count: 4,753
Modeled Residue Count: 539
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE A	A	540	Serratia marcescens	Mutation(s): 0 EC: 3.2.1.14
UniProt
Find proteins for P07254 (Serratia marcescens) Explore P07254 Go to UniProtKB: P07254
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07254
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose-(1-4)-2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose	B, C	2	N/A	N/A	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G32359JL GlyCosmos: G32359JL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGT Query on NGT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL C₈ H₁₃ N O₄ S DRHXTSWSUAJOJZ-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.215 (Depositor), 0.199 (DCC)
R-Value Work: 0.165 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.214	α = 90
b = 200.97	β = 90
c = 59.437	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-10-12
Changes: Database references, Derived calculations, Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary