SMTL ID : 5tmf.1

Re-refinement of thermus thermophilus RNA polymerase

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, L.85, V.86, V.170, F.171, S.172, D.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.51, A:D.202, A:D.202 PO4.5: 2 residues within 4Å: Chain D: D.952, Y.1015 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.952, D:D.952

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)

NE6.2: 16 residues within 4Å: Chain C: F.1032, E.1034, V.1037, W.1038, E.1041, L.1053, S.1084 Chain D: F.614, L.619, G.620, K.621, V.1099, H.1103, A.1438, K.1463, I.1467 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:E.1034, C:L.1053, D:F.614, D:L.619, D:A.1438, D:I.1467, D:I.1467 Hydrogen bonds: C:E.1034, C:S.1084, D:G.620 Salt bridges: D:K.621

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: C.58, C.60, 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.4: 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840 MG.7: 3 residues within 4Å: Chain D: D.739, D.741, D.743 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743

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

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

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

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