SMTL ID : 5tmc.1

Re-refinement of Thermus thermopiles DNA-directed RNA polymerase structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

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

Ligands

1 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.170, F.171, S.172, D.202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.170, A:R.175, A:D.202, A:D.202, A:D.202 Water bridges: A:V.170

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain C: P.793, P.794, G.795, E.796, K.1004 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:P.793, C:P.794, C:G.795, C:E.796 MG.3: 3 residues within 4Å: Chain C: E.685 Chain D: D.739 Ligands: G4P.7 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain D: D.739, D.741, D.743 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.741, D:D.743, H2O.5 MG.8: 2 residues within 4Å: Chain D: K.908 Ligands: G4P.7 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain D: C.58, 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.5: 5 residues within 4Å: Chain D: C.1112, C.1194, Q.1195, 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 G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.7: 10 residues within 4Å: Chain C: S.878, R.879 Chain D: N.737, R.783, K.908, R.1029, E.1231, Q.1235 Ligands: MG.3, MG.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.737, D:Q.1235, C:S.878 Water bridges: D:K.908, D:K.908, D:K.908, D:Q.1034 Salt bridges: D:R.783, D:K.908, D:K.908, D:R.1029, D:E.1231, C:R.879

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J., On the validation of crystallographic symmetry and the quality of structures. Protein Sci. (2015)

Release Date

2016-11-23

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor SigA: F
unknown protein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
Z

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

unknown protein

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