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- EMDB-71793: Structure of ACP domain conjugated with stearic acid and interact... -

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Basic information

Entry
Database: EMDB / ID: EMD-71793
TitleStructure of ACP domain conjugated with stearic acid and interacting with MPT domain from M. tuberculosis type-I FAS
Map dataMain sharpened map
Sample
  • Complex: Fatty acid synthase
    • Protein or peptide: 3-oxoacyl-ACP synthase
    • Protein or peptide: Fatty acid synthase
KeywordsFatty acid synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


fatty acid synthase complex / beta-ketoacyl-[acyl-carrier-protein] synthase I / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid synthase activity / fatty acid biosynthetic process / hydrolase activity
Similarity search - Function
: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / : / : / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain ...: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / : / : / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-ACP synthase / Fatty acid synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsMazhab-Jafari MT / Samani EK
Funding support Canada, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)195698 Canada
Canadian Institutes of Health Research (CIHR)419240 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06070 Canada
CitationJournal: To Be Published
Title: Structural basis of product recognition by Mycobacterium Tuberculosis fatty acid synthase
Authors: Samani EK / Mazhab-Jafari MT
History
DepositionJul 23, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71793.png

Downloads & links

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Map

FileDownload / File: emd_71793.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 380 pix.
= 353.4 Å		0.93 Å/pix.
x 380 pix.
= 353.4 Å		0.93 Å/pix.
x 380 pix.
= 353.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.44080326 - 0.70603865
Average (Standard dev.)0.002622916 (±0.01871843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 353.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_71793_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_71793_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fatty acid synthase

EntireName: Fatty acid synthase
Components
  • Complex: Fatty acid synthase
    • Protein or peptide: 3-oxoacyl-ACP synthase
    • Protein or peptide: Fatty acid synthase

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Supramolecule #1: Fatty acid synthase

SupramoleculeName: Fatty acid synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: 3-oxoacyl-ACP synthase

MacromoleculeName: 3-oxoacyl-ACP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: beta-ketoacyl-[acyl-carrier-protein] synthase I
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 326.601562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTIHEHDRVS ADRGGDSPHT THALVDRLMA GEPYAVAFGG QGSAWLETLE ELVSATGIET ELATLVGEAE LLLDPVTDEL IVVRPIGFE PLQWVRALAA EDPVPSDKHL TSAAVSVPGV LLTQIAATRA LARQGMDLVA TPPVAMAGHS QGVLAVEALK A GGARDVEL ...String:
MTIHEHDRVS ADRGGDSPHT THALVDRLMA GEPYAVAFGG QGSAWLETLE ELVSATGIET ELATLVGEAE LLLDPVTDEL IVVRPIGFE PLQWVRALAA EDPVPSDKHL TSAAVSVPGV LLTQIAATRA LARQGMDLVA TPPVAMAGHS QGVLAVEALK A GGARDVEL FALAQLIGAA GTLVARRRGI SVLGDRPPMV SVTNADPERI GRLLDEFAQD VRTVLPPVLS IRNGRRAVVI TG TPEQLSR FELYCRQISE KEEADRKNKV RGGDVFSPVF EPVQVEVGFH TPRLSDGIDI VAGWAEKAGL DVALARELAD AIL IRKVDW VDEITRVHAA GARWILDLGP GDILTRLTAP VIRGLGIGIV PAATRGGQRN LFTVGATPEV ARAWSSYAPT VVRL PDGRV KLSTKFTRLT GRSPILLAGM TPTTVDAKIV AAAANAGHWA ELAGGGQVTE EIFGNRIEQM AGLLEPGRTY QFNAL FLDP YLWKLQVGGK RLVQKARQSG AAIDGVVISA GIPDLDEAVE LIDELGDIGI SHVVFKPGTI EQIRSVIRIA TEVPTK PVI MHVEGGRAGG HHSWEDLDDL LLATYSELRS RANITVCVGG GIGTPRRAAE YLSGRWAQAY GFPLMPIDGI LVGTAAM AT KESTTSPSVK RMLVDTQGTD QWISAGKAQG GMASSRSQLG ADIHEIDNSA SRCGRLLDEV AGDAEAVAER RDEIIAAM A KTAKPYFGDV ADMTYLQWLR RYVELAIGEG NSTADTASVG SPWLADTWRD RFEQMLQRAE ARLHPQDFGP IQTLFTDAG LLDNPQQAIA ALLARYPDAE TVQLHPADVP FFVTLCKTLG KPVNFVPVID QDVRRWWRSD SLWQAHDARY DADAVCIIPG TASVAGITR MDEPVGELLD RFEQAAIDEV LGAGVEPKDV ASRRLGRADV AGPLAVVLDA PDVRWAGRTV TNPVHRIADP A EWQVHDGP ENPRATHSST GARLQTHGDD VALSVPVSGT WVDIRFTLPA NTVDGGTPVI ATEDATSAMR TVLAIAAGVD SP EFLPAVA NGTATLTVDW HPERVADHTG VTATFGEPLA PSLTNVPDAL VGPCWPAVFA AIGSAVTDTG EPVVEGLLSL VHL DHAARV VGQLPTVPAQ LTVTATAANA TDTDMGRVVP VSVVVTGADG AVIATLEERF AILGRTGSAE LADPARAGGA VSAN ATDTP RRRRRDVTIT APVDMRPFAV VSGDHNPIHT DRAAALLAGL ESPIVHGMWL SAAAQHAVTA TDGQARPPAR LVGWT ARFL GMVRPGDEVD FRVERVGIDQ GAEIVDVAAR VGSDLVMSAS ARLAAPKTVY AFPGQGIQHK GMGMEVRARS KAARKV WDT ADKFTRDTLG FSVLHVVRDN PTSIIASGVH YHHPDGVLYL TQFTQVAMAT VAAAQVAEMR EQGAFVEGAI ACGHSVG EY TALACVTGIY QLEALLEMVF HRGSKMHDIV PRDELGRSNY RLAAIRPSQI DLDDADVPAF VAGIAESTGE FLEIVNFN L RGSQYAIAGT VRGLEALEAE VERRRELTGG RRSFILVPGI DVPFHSRVLR VGVAEFRRSL DRVMPRDADP DLIIGRYIP NLVPRLFTLD RDFIQEIRDL VPAEPLDEIL ADYDTWLRER PREMARTVFI ELLAWQFASP VRWIETQDLL FIEEAAGGLG VERFVEIGV KSSPTVAGLA TNTLKLPEYA HSTVEVLNAE RDAAVLFATD TDPEPEPEED EPVAESPAPD VVSEAAPVAP A ASSAGPRP DDLVFDAADA TLALIALSAK MRIDQIEELD SIESITDGAS SRRNQLLVDL GSELNLGAID GAAESDLAGL RS QVTKLAR TYKPYGPVLS DAINDQLRTV LGPSGKRPGA IAERVKKTWE LGEGWAKHVT VEVALGTREG SSVRGGAMGH LHE GALADA ASVDKVIDAA VASVAARQGV SVALPSAGSG GGATIDAAAL SEFTDQITGR EGVLASAARL VLGQLGLDDP VNAL PAAPD SELIDLVTAE LGADWPRLVA PVFDPKKAVV FDDRWASARE DLVKLWLTDE GDIDADWPRL AERFEGAGHV VATQA TWWQ GKSLAAGRQI HASLYGRIAA GAENPEPGRY GGEVAVVTGA SKGSIAASVV ARLLDGGATV IATTSKLDEE RLAFYR TLY RDHARYGAAL WLVAANMASY SDVDALVEWI GTEQTESLGP QSIHIKDAQT PTLLFPFAAP RVVGDLSEAG SRAEMEM KV LLWAVQRLIG GLSTIGAERD IASRLHVVLP GSPNRGMFGG DGAYGEAKSA LDAVVSRWHA ESSWAARVSL AHALIGWT R GTGLMGHNDA IVAAVEEAGV TTYSTDEMAA LLLDLCDAES KVAAARSPIK ADLTGGLAEA NLDMAELAAK AREQMSAAA AVDEDAEAPG AIAALPSPPR GFTPAPPPQW DDLDVDPADL VVIVGGAEIG PYGSSRTRFE MEVENELSAA GVLELAWTTG LIRWEDDPQ PGWYDTESGE MVDESELVQR YHDAVVQRVG IREFVDDGAI DPDHASPLLV SVFLEKDFAF VVSSEADARA F VEFDPEHT VIRPVPDSTD WQVIRKAGTE IRVPRKTKLS RVVGGQIPTG FDPTVWGISA DMAGSIDRLA VWNMVATVDA FL SSGFSPA EVMRYVHPSL VANTQGTGMG GGTSMQTMYH GNLLGRNKPN DIFQEVLPNI IAAHVVQSYV GSYGAMIHPV AAC ATAAVS VEEGVDKIRL GKAQLVVAGG LDDLTLEGII GFGDMAATAD TSMMCGRGIH DSKFSRPNDR RRLGFVEAQG GGTI LLARG DLALRMGLPV LAVVAFAQSF GDGVHTSIPA PGLGALGAGR GGKDSPLARA LAKLGVAADD VAVISKHDTS TLAND PNET ELHERLADAL GRSEGAPLFV VSQKSLTGHA KGGAAVFQMM GLCQILRDGV IPPNRSLDCV DDELAGSAHF VWVRDT LRL GGKFPLKAGM LTSLGFGHVS GLVALVHPQA FIASLDPAQR ADYQRRADAR LLAGQRRLAS AIAGGAPMYQ RPGDRRF DH HAPERPQEAS MLLNPAARLG DGEAYIG

UniProtKB: 3-oxoacyl-ACP synthase

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Macromolecule #2: Fatty acid synthase

MacromoleculeName: Fatty acid synthase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 327.222375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTIHEHDRVS ADRGGDSPHT THALVDRLMA GEPYAVAFGG QGSAWLETLE ELVSATGIET ELATLVGEAE LLLDPVTDEL IVVRPIGFE PLQWVRALAA EDPVPSDKHL TSAAVSVPGV LLTQIAATRA LARQGMDLVA TPPVAMAGHS QGVLAVEALK A GGARDVEL ...String:
MTIHEHDRVS ADRGGDSPHT THALVDRLMA GEPYAVAFGG QGSAWLETLE ELVSATGIET ELATLVGEAE LLLDPVTDEL IVVRPIGFE PLQWVRALAA EDPVPSDKHL TSAAVSVPGV LLTQIAATRA LARQGMDLVA TPPVAMAGHS QGVLAVEALK A GGARDVEL FALAQLIGAA GTLVARRRGI SVLGDRPPMV SVTNADPERI GRLLDEFAQD VRTVLPPVLS IRNGRRAVVI TG TPEQLSR FELYCRQISE KEEADRKNKV RGGDVFSPVF EPVQVEVGFH TPRLSDGIDI VAGWAEKAGL DVALARELAD AIL IRKVDW VDEITRVHAA GARWILDLGP GDILTRLTAP VIRGLGIGIV PAATRGGQRN LFTVGATPEV ARAWSSYAPT VVRL PDGRV KLSTKFTRLT GRSPILLAGM TPTTVDAKIV AAAANAGHWA ELAGGGQVTE EIFGNRIEQM AGLLEPGRTY QFNAL FLDP YLWKLQVGGK RLVQKARQSG AAIDGVVISA GIPDLDEAVE LIDELGDIGI SHVVFKPGTI EQIRSVIRIA TEVPTK PVI MHVEGGRAGG HHSWEDLDDL LLATYSELRS RANITVCVGG GIGTPRRAAE YLSGRWAQAY GFPLMPIDGI LVGTAAM AT KESTTSPSVK RMLVDTQGTD QWISAGKAQG GMASSRSQLG ADIHEIDNSA SRCGRLLDEV AGDAEAVAER RDEIIAAM A KTAKPYFGDV ADMTYLQWLR RYVELAIGEG NSTADTASVG SPWLADTWRD RFEQMLQRAE ARLHPQDFGP IQTLFTDAG LLDNPQQAIA ALLARYPDAE TVQLHPADVP FFVTLCKTLG KPVNFVPVID QDVRRWWRSD SLWQAHDARY DADAVCIIPG TASVAGITR MDEPVGELLD RFEQAAIDEV LGAGVEPKDV ASRRLGRADV AGPLAVVLDA PDVRWAGRTV TNPVHRIADP A EWQVHDGP ENPRATHSST GARLQTHGDD VALSVPVSGT WVDIRFTLPA NTVDGGTPVI ATEDATSAMR TVLAIAAGVD SP EFLPAVA NGTATLTVDW HPERVADHTG VTATFGEPLA PSLTNVPDAL VGPCWPAVFA AIGSAVTDTG EPVVEGLLSL VHL DHAARV VGQLPTVPAQ LTVTATAANA TDTDMGRVVP VSVVVTGADG AVIATLEERF AILGRTGSAE LADPARAGGA VSAN ATDTP RRRRRDVTIT APVDMRPFAV VSGDHNPIHT DRAAALLAGL ESPIVHGMWL SAAAQHAVTA TDGQARPPAR LVGWT ARFL GMVRPGDEVD FRVERVGIDQ GAEIVDVAAR VGSDLVMSAS ARLAAPKTVY AFPGQGIQHK GMGMEVRARS KAARKV WDT ADKFTRDTLG FSVLHVVRDN PTSIIASGVH YHHPDGVLYL TQFTQVAMAT VAAAQVAEMR EQGAFVEGAI ACGHSVG EY TALACVTGIY QLEALLEMVF HRGSKMHDIV PRDELGRSNY RLAAIRPSQI DLDDADVPAF VAGIAESTGE FLEIVNFN L RGSQYAIAGT VRGLEALEAE VERRRELTGG RRSFILVPGI DVPFHSRVLR VGVAEFRRSL DRVMPRDADP DLIIGRYIP NLVPRLFTLD RDFIQEIRDL VPAEPLDEIL ADYDTWLRER PREMARTVFI ELLAWQFASP VRWIETQDLL FIEEAAGGLG VERFVEIGV KSSPTVAGLA TNTLKLPEYA HSTVEVLNAE RDAAVLFATD TDPEPEPEED EPVAESPAPD VVSEAAPVAP A ASSAGPRP DDLVFDAADA TLALIALSAK MRIDQIEELD SIESITDGA(A1CJI) SRRNQLLVDL GSELNLGAID GAAESD LAG LRSQVTKLAR TYKPYGPVLS DAINDQLRTV LGPSGKRPGA IAERVKKTWE LGEGWAKHVT VEVALGTREG SSVRGGA MG HLHEGALADA ASVDKVIDAA VASVAARQGV SVALPSAGSG GGATIDAAAL SEFTDQITGR EGVLASAARL VLGQLGLD D PVNALPAAPD SELIDLVTAE LGADWPRLVA PVFDPKKAVV FDDRWASARE DLVKLWLTDE GDIDADWPRL AERFEGAGH VVATQATWWQ GKSLAAGRQI HASLYGRIAA GAENPEPGRY GGEVAVVTGA SKGSIAASVV ARLLDGGATV IATTSKLDEE RLAFYRTLY RDHARYGAAL WLVAANMASY SDVDALVEWI GTEQTESLGP QSIHIKDAQT PTLLFPFAAP RVVGDLSEAG S RAEMEMKV LLWAVQRLIG GLSTIGAERD IASRLHVVLP GSPNRGMFGG DGAYGEAKSA LDAVVSRWHA ESSWAARVSL AH ALIGWTR GTGLMGHNDA IVAAVEEAGV TTYSTDEMAA LLLDLCDAES KVAAARSPIK ADLTGGLAEA NLDMAELAAK ARE QMSAAA AVDEDAEAPG AIAALPSPPR GFTPAPPPQW DDLDVDPADL VVIVGGAEIG PYGSSRTRFE MEVENELSAA GVLE LAWTT GLIRWEDDPQ PGWYDTESGE MVDESELVQR YHDAVVQRVG IREFVDDGAI DPDHASPLLV SVFLEKDFAF VVSSE ADAR AFVEFDPEHT VIRPVPDSTD WQVIRKAGTE IRVPRKTKLS RVVGGQIPTG FDPTVWGISA DMAGSIDRLA VWNMVA TVD AFLSSGFSPA EVMRYVHPSL VANTQGTGMG GGTSMQTMYH GNLLGRNKPN DIFQEVLPNI IAAHVVQSYV GSYGAMI HP VAACATAAVS VEEGVDKIRL GKAQLVVAGG LDDLTLEGII GFGDMAATAD TSMMCGRGIH DSKFSRPNDR RRLGFVEA Q GGGTILLARG DLALRMGLPV LAVVAFAQSF GDGVHTSIPA PGLGALGAGR GGKDSPLARA LAKLGVAADD VAVISKHDT STLANDPNET ELHERLADAL GRSEGAPLFV VSQKSLTGHA KGGAAVFQMM GLCQILRDGV IPPNRSLDCV DDELAGSAHF VWVRDTLRL GGKFPLKAGM LTSLGFGHVS GLVALVHPQA FIASLDPAQR ADYQRRADAR LLAGQRRLAS AIAGGAPMYQ R PGDRRFDH HAPERPQEAS MLLNPAARLG DGEAYIG

UniProtKB: Fatty acid synthase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 458280
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6gjc

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45089
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

6gjc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9pqy:
Structure of ACP domain conjugated with stearic acid and interacting with MPT domain from M. tuberculosis type-I FAS

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