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X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter

Analyse X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7S01
Type: protein + DNA
Length: 2,723 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase beta' subunit…
EC: 2.7.7.6
UniProt: A0A172JIC8, A0A172JIH0, A0A172JI16, A0A172JI62, A0A172JHZ2
Ligands: UMP, DG, DT, DA, ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 9 distinct chains · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit	protein	463	65% helix, 5% strand	A0A172JIC8
d	DNA-directed RNA polymerase beta' subunit	protein	426	40% helix, 18% strand	A0A172JIH0
c	DNA-directed RNA polymerase beta subunit	protein	484	39% helix, 22% strand	A0A172JI16
D	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	631	46% helix, 15% strand	A0A172JI62
C	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	649	32% helix, 25% strand	A0A172JHZ2
N	Non-template strand of the forked DNA oligonucleotide (downstream copy)	dna	13	—	—
T	Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif	dna	21	—	—
t	Non-template strand of the forked DNA oligonucleotide (downstream copy)	dna	14	—	—
n	Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif	dna	22	—	—

Ligands and binding sites

UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 5 copies · chains A, d, t, c, C, T
DG · 2'-deoxyguanosine-5'-monophosphate · ligand · chains A, c
DT · Thymidine-5'-monophosphate · ligand · chains t, n
DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains A, n
ZN · Zinc ion · metal · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	574	0.85	0.90	62	empty
2	941	0.76	0.79	76	empty
3	232	0.76	0.90	30	empty
4	252	0.75	0.89	51	empty
5	686	0.75	0.81	55	empty

Interfaces

22 interfaces between chains.

d–C · 5320 Å² buried · 49 hydrogen bonds · protein-protein
c–C · 3611 Å² buried · 39 hydrogen bonds · protein-protein
D–C · 3585 Å² buried · 38 hydrogen bonds · protein-protein
d–D · 3373 Å² buried · 32 hydrogen bonds · protein-protein
A–d · 2668 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7S01 · X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A172JIC8
Every structure of UniProt A0A172JIH0
Every structure of UniProt A0A172JI16
Every structure of UniProt A0A172JI62
Every structure of UniProt A0A172JHZ2
Elsewhere: RCSB PDB 7S01 · PDBe 7S01 · UniProt A0A172JIC8 · UniProt A0A172JIH0 · UniProt A0A172JI16 · UniProt A0A172JI62 · UniProt A0A172JHZ2

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