6ACX | pdb_00006acx

Crystal structure of Mycobacterium smegmatis Mfd in complex with ADP + Pi at 3.5 A resolution.

PDB DOI: https://doi.org/10.2210/pdb6ACX/pdb

Classification: HYDROLASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-27 Released: 2019-08-28
Deposition Author(s): Putta, S., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.226 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for nucleotide-mediated remodelling mechanism of Mycobacterium Mfd

Putta, S., Prabha, S., Bhat, V., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.

To be published.

Macromolecule Content

Total Structure Weight: 268.21 kDa
Atom Count: 17,349
Modeled Residue Count: 2,343
Deposited Residue Count: 2,470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobacterium smegmatis Mfd	A, B	1,235	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: mfd EC: 3.6.4
UniProt
Find proteins for A0R3C5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3C5 Go to UniProtKB: A0R3C5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R3C5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]