1T2A

Crystal structure of human GDP-D-mannose 4,6-dehydratase

PDB DOI: https://doi.org/10.2210/pdb1T2A/pdb

Classification: STRUCTURAL GENOMICS,LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-04-20 Released: 2004-05-10
Deposition Author(s): Walker, J.R., Vedadi, M., Sharma, S., Houston, S., Wasney, G., Loppnau, P., Sundstrom, M., Arrowsmith, C., Edwards, A., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 ?
R-Value Free: 0.212
R-Value Work: 0.173
R-Value Observed: 0.173

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure and Biophysical Characterization of Human GDP-D-mannose 4,6-dehydratase

Vedadi, M., Walker, J.R., Sharma, S., Houston, S., Wasney, G., Loppnau, P., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 175.55 kDa
Atom Count: 12,166
Modelled Residue Count: 1,351
Deposited Residue Count: 1,500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose 4,6 dehydratase	A, B, C, D	375	Homo sapiens	Mutation(s): 0 Gene Names: GMDS EC: 4.2.1.47
UniProt & NIH Common Fund Data Resources
Find proteins for O60547 (Homo sapiens) Explore O60547 Go to UniProtKB: O60547
PHAROS: O60547 GTEx: ENSG00000112699
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60547
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 ?
R-Value Free: 0.212
R-Value Work: 0.173
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 88.595	α = 90
b = 122.064	β = 90
c = 139.403	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-05-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-05-10
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

1T2A

Crystal structure of human GDP-D-mannose 4,6-dehydratase

Crystal Structure and Biophysical Characterization of Human GDP-D-mannose 4,6-dehydratase

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)