7K6C

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC 19977 / DSM 44196 with NADP and inhibitor P218

PDB DOI: https://doi.org/10.2210/pdb7K6C/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Mycobacteroides abscessus ATCC 19977
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-09-19 Released: 2021-03-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.207
R-Value Work: 0.166
R-Value Observed: 0.167

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

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC 19977 / DSM 44196 with NADP and inhibitor P218

Abendroth, J., Santhakumar, V., Walpole, C., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 138.81 kDa
Atom Count: 9,892
Modelled Residue Count: 1,115
Deposited Residue Count: 1,197
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B, C, D, E A, B, C, D, E, F, G	171	Mycobacteroides abscessus ATCC 19977	Mutation(s): 2 Gene Names: MAB_3090c EC: 1.5.1.3
UniProt
Find proteins for B1MD46 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MD46 Go to UniProtKB: B1MD46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1MD46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] H [auth A] K [auth B] P [auth C] T [auth D] CA [auth G], H [auth A], K [auth B], P [auth C], T [auth D], W [auth E], Z [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain CA [auth G] Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
MMV (Subject of Investigation/LOI) Query on MMV Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain X [auth E] SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain I [auth A] MOL2 format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain I [auth A] mmCIF format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	AA [auth F] DA [auth G] I [auth A] L [auth B] Q [auth C] AA [auth F], DA [auth G], I [auth A], L [auth B], Q [auth C], U [auth D], X [auth E]	3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid C₁₈ H₂₄ N₄ O₄ VDGXZSSDCDPCRF-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] EA [auth G] M [auth B] R [auth C] V [auth D] BA [auth F], EA [auth G], M [auth B], R [auth C], V [auth D], Y [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C]	J [auth A], N [auth B], O [auth B], S [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C]