1MV8

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb1MV8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-09-24 Released: 2003-05-06
Deposition Author(s): Snook, C.F., Tipton, P.A., Beamer, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.194
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 196.68 kDa
Atom Count: 14,879
Modelled Residue Count: 1,744
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose 6-dehydrogenase	A, B, C, D	436	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: AlgD EC: 1.1.1.132
UniProt
Find proteins for P11759 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P11759 Go to UniProtKB: P11759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11759
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F	2		N/A	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D]	G [auth A], J [auth B], K [auth C], O [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth D]
GDX Query on GDX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D]	H [auth A], I [auth A], P [auth D], Q [auth D]	GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER C₁₆ H₂₃ N₅ O₁₇ P₂ DNBSDUDYNPJVCN-ZXTXFPBHSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth D] Focus chain Q [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C]	N [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C]	L [auth C], M [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain L [auth C] Focus chain M [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	E, F	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.194
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.472	α = 90
b = 82.472	β = 90
c = 309.893	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-05-06

Deposition Author(s):

Snook, C.F.

Tipton, P.A.

Beamer, L.J.

Revision History (Full details and data files)

Version 1.0: 2003-05-06
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2014-11-12
Changes: Structure summary
Version 1.4: 2018-02-14
Changes: Experimental preparation
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-02-14
Changes: Data collection, Database references, Refinement description, Structure summary

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1MV8

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2