9N07 | pdb_00009n07

Deposited: 2025-01-23 Released: 2025-10-15
Deposition Author(s): Brewer, J.J., Darst, S.A., Campbell, E.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription-repair-coupling factor	A	1,166	Escherichia coli	Mutation(s): 0 Gene Names: mfd, ACU57_04350, BGM66_002106, CTR35_002399, E4K51_18465, EIZ93_13025, FOI11_007375, FOI11_14345, FWK02_07210, GP944_10720... mfd, ACU57_04350, BGM66_002106, CTR35_002399, E4K51_18465, EIZ93_13025, FOI11_007375, FOI11_14345, FWK02_07210, GP944_10720, GP979_06075, GRW05_02535, HMV95_16245, J0541_003194, JNP96_10835 EC: 3.6.4
UniProt
Find proteins for P30958 (Escherichia coli (strain K12)) Explore P30958 Go to UniProtKB: P30958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30958
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	B [auth G], C [auth H]	234	Escherichia coli	Mutation(s): 0 Gene Names: rpoA, FTV90_00720, FTV93_20930 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4 Go to UniProtKB: P0A7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Z4
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	D [auth I]	1,340	Escherichia coli	Mutation(s): 0 Gene Names: rpoB EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2 Go to UniProtKB: P0A8V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8V2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	E [auth J]	1,359	Escherichia coli	Mutation(s): 0 Gene Names: rpoC, NOI85_25215 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7 Go to UniProtKB: P0A8T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8T7
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	F [auth K]	91	Escherichia coli	Mutation(s): 0 Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800 Go to UniProtKB: P0A800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A800
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
DNA (49-MER)	G [auth N]	64	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
RNA (5'-R(PGPGPAPGPAPGPGPUP*A)-3')	H [auth R]	20	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
DNA (55-MER)	I [auth T]	64	synthetic construct
Sequence Annotations Expand
Reference Sequence

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth J] SDF format, chain N [auth J] MOL2 format, chain M [auth J] MOL2 format, chain N [auth J] mmCIF format, chain M [auth J] mmCIF format, chain N [auth J]	M [auth J], N [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth J] Focus chain N [auth J] Interactions & Density Focus chain M [auth J] Focus chain N [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth J] MOL2 format, chain L [auth J] mmCIF format, chain L [auth J]	L [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth J] Interactions & Density Focus chain L [auth J]