4S1O | pdb_00004s1o

Structure of Mycobacterium tuberculosis NadD in complex with NADP

PDB DOI: https://doi.org/10.2210/pdb4S1O/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-01-14 Released: 2016-01-20
Deposition Author(s): Korotkov, K.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.194 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Mycobacterium tuberculosis protein

Korotkov, K.V.

To be published.

Macromolecule Content

Total Structure Weight: 46.26 kDa
Atom Count: 3,047
Modeled Residue Count: 346
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nicotinate-nucleotide adenylyltransferase	A, B	201	Mycobacterium tuberculosis H37Rv	Mutation(s): 2 Gene Names: LH57_13225, nadD, P425_02519, Rv2421c, RVBD_2421c EC: 2.7.7.18
UniProt
Find proteins for P9WJJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJJ5 Go to UniProtKB: P9WJJ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WJJ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.234 (Depositor), 0.240 (DCC)
R-Value Work: 0.194 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.06	α = 90
b = 66.06	β = 90
c = 165.21	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Korotkov, K.V.

Revision History (Full details and data files)

Version 1.0: 2016-01-20
Type: Initial release
Version 1.1: 2016-01-27
Changes: Other
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Structure of Mycobacterium tuberculosis NadD in complex with NADP

Structure of Mycobacterium tuberculosis protein

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations