4R16

Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb4R16/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-04 Released: 2015-10-14
Deposition Author(s): Pampa, K.J., Lokanath, N.K., Rai, R.V., Kunishima, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.251
R-Value Work: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii

Pampa, K.J., Lokanath, N.K., Rai, R.V., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 94.48 kDa
Atom Count: 7,590
Modelled Residue Count: 836
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
418aa long hypothetical UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase	A, B	418	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH1618 EC: 1.1.1.336
UniProt
Find proteins for O59284 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59284 Go to UniProtKB: O59284
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O59284
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAJ Query on SAJ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(2S,3S,4R,5S,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxane-2-carboxylic acid C₁₇ H₂₅ N₃ O₁₈ P₂ DZOGQXKQLXAPND-XHUKORKBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.251
R-Value Work: 0.224
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.03	α = 66.2
b = 74.65	β = 70.4
c = 73.56	γ = 75.2

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.