SMTL ID : 3dxj.1 (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

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: T.51, A.52, K.83, E.84, L.85, V.86, V.170, R.175, D.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.51, A:D.202 Salt bridges: A:K.83, A:R.175 PO4.8: 8 residues within 4Å: Chain C: E.1034 Chain D: F.614, R.615, R.1096, D.1100, S.1439, F.1440, K.1463 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.1100 Salt bridges: D:R.1096, D:K.1463 Water bridges: C:E.1034

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840, Y.841, V.842 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:K.840, B:D.168, H2O.1 MG.7: 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

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

MPD.3: 5 residues within 4Å: Chain C: G.951, L.952, Q.969 Chain D: D.952, Y.1015 No protein-ligand interaction detected (PLIP) MPD.4: 2 residues within 4Å: Chain C: Y.895, F.896 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.895 Hydrogen bonds: C:Y.895

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain D: C.58, C.60, K.62, Y.63, 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.6: 6 residues within 4Å: Chain D: C.1112, C.1194, Q.1195, T.1196, 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 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)

NE6.9: 19 residues within 4Å: Chain C: F.1032, V.1037, W.1038, E.1041, L.1053, S.1084, L.1088 Chain D: F.614, L.618, L.619, G.620, V.1099, D.1100, H.1103, A.1438, S.1439, T.1443, K.1463, I.1467 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.1438, D:T.1443, D:I.1467, C:L.1053, C:L.1088 Hydrogen bonds: D:G.620, C:S.1084 Salt bridges: D:K.621 Water bridges: C:E.1034

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
A

B
B

C
C

D
D

E
E

F
F

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

Related Entries With Identical Sequence