SMTL ID : 2waq.1

The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

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

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.58, C.61, C.68, H.71 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.58, A:C.61, A:C.68, A:C.68, A:H.71 ZN.2: 4 residues within 4Å: Chain A: C.98, C.101, V.145, C.146 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.98, A:C.101, A:V.145, A:C.146 ZN.3: 2 residues within 4Å: Chain A: H.426 Chain C: E.80 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:E.80, C:E.80, A:H.426, A:H.426 ZN.5: 5 residues within 4Å: Chain B: C.1064, C.1067, C.1082, I.1084, S.1089 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.1064, B:C.1067 ZN.6: 4 residues within 4Å: Chain B: R.174, H.570, N.572, E.622 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.570 ZN.7: 3 residues within 4Å: Chain B: R.694, H.696, H.997 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.696 ZN.8: 2 residues within 4Å: Chain C: E.348, H.353 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.353 ZN.10: 5 residues within 4Å: Chain K: C.7, T.9, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.44, K:C.45 ZN.11: 4 residues within 4Å: Chain L: C.9, T.12, C.26, C.29 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.9, L:T.12, L:C.26, L:C.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.456, D.458, D.460 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.456, A:D.456, A:D.458, A:D.460

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.9: 11 residues within 4Å: Chain D: C.183, P.184, E.185, V.187, F.188, C.203, L.205, C.206, E.207, C.209, I.219 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.203, D:C.206, D:C.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korkhin, Y. et al., Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. Plos Biol. (2009)

Release Date

2009-05-19

Peptides

DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT: A
DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT: B
DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT: C
DNA-DIRECTED RNA POLYMERASE RPO3 SUBUNIT: D
DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT: E
DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT: F
DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT: G
DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT: H
DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT: I
DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT: J
DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT: K
DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT: L
DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
K

J
L

K
N

L
P

M
Q

DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO3 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT

DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT

Related Entries With Identical Sequence