SMTL ID : 2ppb.1 (1 other biounit)

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-1-1-1-mer

Ligands

1 x STD: STREPTOLYDIGIN(Non-covalent)

STD.1: 13 residues within 4Å: Chain C: G.4 Chain F: R.422, F.425, R.428, A.447, I.449 Chain G: A.1082, A.1085, L.1086, R.1087, D.1090, P.1257, I.1260 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:A.1085, G:L.1086, G:L.1086, G:L.1086, G:P.1257, F:R.422, F:F.425 Hydrogen bonds: G:R.1087, G:D.1090

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain G: C.58, C.60, C.73, C.76 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.58, G:C.60, G:C.73, G:C.76 ZN.3: 4 residues within 4Å: Chain G: C.1112, C.1194, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.1112, G:C.1194, G:C.1201, G:C.1204

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: G.16 Chain G: D.739, D.741, D.743 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.739, G:D.741, G:D.741, G:D.743 MG.5: 2 residues within 4Å: Chain G: D.739 Ligands: APC.6 No protein-ligand interaction detected (PLIP)

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.6: 11 residues within 4Å: Chain A: T.14 Chain B: G.16 Chain F: R.557, R.879 Chain G: R.704, P.706, N.737, R.783, R.1029, T.1088 Ligands: MG.5 11 PLIP interactions: 7 interactions with chain G, 4 interactions with chain F Hydrogen bonds: G:R.704, G:N.737, G:R.783, G:T.1088, F:R.557, F:R.557 Water bridges: G:R.1029, G:R.1029 Salt bridges: G:R.1029, F:R.557, F:R.879

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vassylyev, D.G. et al., Structural basis for substrate loading in bacterial RNA polymerase. Nature (2007)

Release Date

2007-07-17

Peptides

DNA-directed RNA polymerase alpha chain: DE
DNA-directed RNA polymerase beta chain: F
DNA-directed RNA polymerase beta' chain: G
DNA-directed RNA polymerase omega chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
D

H
E

DNA-directed RNA polymerase alpha chain

DNA-directed RNA polymerase beta chain

DNA-directed RNA polymerase beta' chain

DNA-directed RNA polymerase omega chain

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