9MVA | pdb_00009mva

Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA

PDB DOI: https://doi.org/10.2210/pdb9MVA/pdb

Classification: ANTIBIOTIC
Organism(s): Mycobacteroides abscessus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-15 Released: 2025-01-29
Deposition Author(s): Jayasinghe, T.D., Coker, A.L., Rajendra, T., Miller, D., Lee, R.E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.222 (Depositor), 0.205 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA

Jayasinghe, T.D., Coker, A.L., Rajendra, T., Miller, D., Lee, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 280.76 kDa
Atom Count: 22,281
Modeled Residue Count: 2,452
Deposited Residue Count: 2,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amikacin resistance N-acetyltransferase Eis2	A, B, C, D, E A, B, C, D, E, F	412	Mycobacteroides abscessus	Mutation(s): 0 Gene Names: eis_2, D2E76_13785, DDJ47_01400, ERS075604_03569

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SOP (Subject of Investigation/LOI) Query on SOP Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DB [auth F] SDF format, chain H [auth A] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain TA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth E]	AA [auth C] DB [auth F] H [auth A] JA [auth D] P [auth B] AA [auth C], DB [auth F], H [auth A], JA [auth D], P [auth B], TA [auth E]	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE C₂₄ H₄₀ N₇ O₁₇ P₃ S GAMKENBUYYJLCQ-NDZSKPAWSA-N		Interactions Focus chain AA [auth C] Focus chain DB [auth F] Focus chain H [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain TA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain DB [auth F] Focus chain H [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain TA [auth E]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain EB [auth F] SDF format, chain I [auth A] SDF format, chain WA [auth E] SDF format, chain YA [auth E] SDF format, chain VA [auth E] SDF format, chain R [auth B] SDF format, chain KA [auth D] SDF format, chain IB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain WA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain IB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain I [auth A] mmCIF format, chain WA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain IB [auth F]	CA [auth C] EB [auth F] I [auth A] IB [auth F] KA [auth D] CA [auth C], EB [auth F], I [auth A], IB [auth F], KA [auth D], R [auth B], VA [auth E], WA [auth E], YA [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain EB [auth F] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain R [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain YA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain EB [auth F] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain R [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain YA [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain GB [auth F] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain XA [auth E] SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain HB [auth F] SDF format, chain FB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain FB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain JB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain HB [auth F] mmCIF format, chain FB [auth F]	DA [auth C] EA [auth C] FB [auth F] GB [auth F] HB [auth F] DA [auth C], EA [auth C], FB [auth F], GB [auth F], HB [auth F], J [auth A], JB [auth F], K [auth A], LA [auth D], MA [auth D], NA [auth D], Q [auth B], S [auth B], T [auth B], U [auth B], UA [auth E], XA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain XA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain XA [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain G [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain SA [auth E] SDF format, chain Z [auth C] SDF format, chain CB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain CB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain Z [auth C] mmCIF format, chain CB [auth F]	BA [auth C] CB [auth F] G [auth A] IA [auth D] O [auth B] BA [auth C], CB [auth F], G [auth A], IA [auth D], O [auth B], SA [auth E], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain SA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain SA [auth E] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain KB [auth F] SDF format, chain OA [auth D] SDF format, chain V [auth B] SDF format, chain ZA [auth E] SDF format, chain L [auth A] SDF format, chain FA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain OA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain FA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain OA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain FA [auth C]	FA [auth C] KB [auth F] L [auth A] OA [auth D] V [auth B] FA [auth C], KB [auth F], L [auth A], OA [auth D], V [auth B], ZA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain KB [auth F] Focus chain L [auth A] Focus chain OA [auth D] Focus chain V [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain KB [auth F] Focus chain L [auth A] Focus chain OA [auth D] Focus chain V [auth B] Focus chain ZA [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MB [auth F] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain N [auth A] SDF format, chain BB [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth F] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain N [auth A] MOL2 format, chain BB [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth F] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain N [auth A] mmCIF format, chain BB [auth E]	AB [auth E] BB [auth E] GA [auth C] HA [auth C] LB [auth F] AB [auth E], BB [auth E], GA [auth C], HA [auth C], LB [auth F], M [auth A], MB [auth F], N [auth A], PA [auth D], QA [auth D], RA [auth D], W [auth B], X [auth B], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MB [auth F] Focus chain N [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MB [auth F] Focus chain N [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]