SMTL ID : 8rqk.1

Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-2-1-1-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain A: D.415, D.417, D.419 Chain M: N.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.415, A:D.417, A:D.417, A:D.419 MG.6: 2 residues within 4Å: Chain N: U.8, G.9 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain N: U.35, G.36 Chain O: R.120 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain N: G.18, U.19 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: G.42, C.49, T.51, C.52, C.59, G.61, H.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.59, A:H.62 ZN.3: 6 residues within 4Å: Chain A: C.90, H.92, C.93, C.130, N.132, C.135 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.90, A:C.93, A:C.130, A:C.135 ZN.4: 8 residues within 4Å: Chain B: C.1087, N.1089, C.1090, G.1091, C.1103, R.1105, C.1106, P.1113 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1087, B:C.1090, B:C.1103, B:C.1106 ZN.5: 5 residues within 4Å: Chain F: C.326, H.328, C.363, V.365, C.366 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.326, F:H.328, F:C.363, F:C.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grimm, C. et al., Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution. To Be Published

Release Date

2025-01-29

Peptides

DNA-directed RNA polymerase 147 kDa polypeptide: A
DNA-directed RNA polymerase 133 kDa polypeptide: B
DNA-directed RNA polymerase 35 kDa subunit: C
DNA-directed RNA polymerase 22 kDa subunit: D
DNA-directed RNA polymerase 18 kDa subunit: E
RNA polymerase-associated transcription-specificity factor RAP94: F
DNA-directed RNA polymerase 7 kDa subunit: G
Early transcription factor 82 kDa subunit: H
mRNA-capping enzyme regulatory subunit OPG124: I
mRNA-capping enzyme catalytic subunit: J
Core protein OPG073: KL
DNA-directed RNA polymerase 30 kDa polypeptide: M
Nucleoside triphosphatase I: O
DNA-directed RNA polymerase 19 kDa subunit: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
G

F
I

G
J

H
K

I
L

J
O

K
Q

L
R

M
S

O
Y

P
F

DNA-directed RNA polymerase 147 kDa polypeptide

DNA-directed RNA polymerase 133 kDa polypeptide

DNA-directed RNA polymerase 35 kDa subunit

DNA-directed RNA polymerase 22 kDa subunit

DNA-directed RNA polymerase 18 kDa subunit

RNA polymerase-associated transcription-specificity factor RAP94

DNA-directed RNA polymerase 7 kDa subunit

Early transcription factor 82 kDa subunit

mRNA-capping enzyme regulatory subunit OPG124

mRNA-capping enzyme catalytic subunit

Core protein OPG073

DNA-directed RNA polymerase 30 kDa polypeptide

Nucleoside triphosphatase I

DNA-directed RNA polymerase 19 kDa subunit

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