SMTL ID : 3cqz.1

Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

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

Ligands

1 x ILX- TRX- GLY- ILE- GLY- CSX- ASN- HYP: ALPHA-AMANITIN(Non-covalent)

ILX-TRX-GLY-ILE-GLY-CSX-ASN-HYP.1: 25 residues within 4Å: Chain A: V.719, N.723, R.726, D.727, F.755, I.756, A.759, Q.760, C.764, V.765, G.766, Q.767, Q.768, S.769, G.772, K.773, R.774, H.816, G.819, G.820, E.822, N.1082, H.1085, A.1087 Chain B: Q.763 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.719, A:V.719, A:R.726, A:I.756, A:I.756, A:Q.760, A:R.774, A:E.822 Hydrogen bonds: A:N.723, A:N.723, A:R.726, A:Q.760, A:Q.767, A:Q.768, A:S.769, A:E.822, A:H.1085, B:Q.763 pi-Cation interactions: A:R.726, A:R.726

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.3: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.4: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.5: 5 residues within 4Å: Chain C: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95 ZN.6: 4 residues within 4Å: Chain G: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.29, G:C.32 ZN.7: 4 residues within 4Å: Chain G: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.75, G:C.78, G:C.103, G:C.106 ZN.8: 4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.46 ZN.9: 5 residues within 4Å: Chain J: C.31, E.33, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48, J:C.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaplan, C.D. et al., The RNA Polymerase II Trigger Loop Functions in Substrate Selection and is Directly Targeted by Alpha-Amanitin. Mol.Cell (2008)

Release Date

2008-07-22

Peptides

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1: A
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2: B
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3: C
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1: D
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3: F
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9: G
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5: H
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11: I
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
L

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4

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