1UR8

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

PDB DOI: https://doi.org/10.2210/pdb1UR8/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-10-27 Released: 2004-04-27
Deposition Author(s): Vaaje-Kolstad, G., Vasella, A., Peter, M.G., Netter, C., Houston, D.R., Westereng, B., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 113.38 kDa
Atom Count: 8,649
Modelled Residue Count: 994
Deposited Residue Count: 998
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE B	A, B	499	Serratia marcescens	Mutation(s): 0 EC: 3.2.1.14
UniProt
Find proteins for Q54276 (Serratia marcescens) Explore Q54276 Go to UniProtKB: Q54276
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q54276
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G08176ED GlyCosmos: G08176ED

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	H [auth A] I [auth A] J [auth A] Q [auth B] R [auth B] H [auth A], I [auth A], J [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.248
R-Value Work: 0.211
R-Value Observed: 0.211
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.396	α = 90
b = 103.484	β = 90
c = 186.022	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-04-27
Type: Initial release
Version 1.1: 2015-04-15
Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
Version 1.2: 2018-05-02
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

1UR8

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)