3HA3 | pdb_00003ha3

Crystal structure of HMA (MMAA4) from mycobacterium tuberculosis complexed with S-adenosylhomocysteine

PDB DOI: https://doi.org/10.2210/pdb3HA3/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-01 Released: 2009-05-12
Deposition Author(s): Boissier, F., Vaubourgeix, J., Julien, S., Mourey, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.250 (Depositor), 0.267 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

SADAE, a potent bisubstrate inhibitor of mycobacterium tuberculosis mycolic acid methyltransferases

Vaubourgeix, J., Bardou, F., Boissier, F., Julien, S., Constant, P., Ploux, O., Daffe, M., Quemard, A., Mourey, L.

To be published.

Macromolecule Content

Total Structure Weight: 36.91 kDa
Atom Count: 2,345
Modeled Residue Count: 281
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHOXY MYCOLIC ACID SYNTHASE 4	A	318	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: mmaA4, MMAA4 (RV0642C), Rv0642c EC: 2.1.1
UniProt
Find proteins for Q79FX8 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore Q79FX8 Go to UniProtKB: Q79FX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79FX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.250 (Depositor), 0.267 (DCC)
R-Value Work: 0.202 (Depositor)
R-Value Observed: 0.204 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.344	α = 90
b = 57.344	β = 90
c = 203.978	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Vaubourgeix, J.

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.