SMTL ID : 3dxj.2 (1 other biounit)

Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 5 residues within 4Å: Chain C: K.915, L.952, T.954, E.965 Chain D: D.952 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.954 Hydrogen bonds: C:K.915, C:E.965, D:D.952, D:D.952

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain D: C.58, A.59, C.60, G.61, K.62, C.73, C.76 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76 ZN.3: 4 residues within 4Å: Chain D: C.1112, C.1194, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1194, D:C.1201, D:C.1204

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain D: R.704, D.739, D.741, D.743 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, D:D.743, H2O.1

1 x NE6: methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate(Non-covalent)

NE6.5: 18 residues within 4Å: Chain C: V.1037, W.1038, E.1041, S.1084, L.1088 Chain D: F.614, L.619, G.620, K.621, V.1099, H.1103, I.1223, A.1438, T.1443, L.1462, K.1463, V.1466, I.1467 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.614, D:F.614, D:L.619, D:T.1443, D:V.1466, D:I.1467, D:I.1467, C:V.1037, C:L.1088 Hydrogen bonds: D:G.620, C:S.1084 Salt bridges: D:K.621

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukhopadhyay, J. et al., The RNA polymerase "switch region" is a target for inhibitors. Cell(Cambridge,Mass.) (2008)

Release Date

2008-10-14

Peptides

DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L: AB
BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M: C
BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N: D
BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O: E
RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

F
P

DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L

BACTERIAL RNA POLYMERASE BETA SUBUNIT; CHAIN C, M

BACTERIAL RNA POLYMERASE BETA-PRIME SUBUNIT; CHAIN D, N

BACTERIAL RNA POLYMERASE OMEGA SUBUNIT; CHAIN E, O

RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P

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