RNA-directed RNA polymerase nsp12 (Pol) | P0DTD1 PRO_0000449629

Model 02

Structure Assessment

Oligo-State: Monomer

GMQE: 0.88

QMEANDisCo Global:: 0.87 ± 0.05

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

6m71.1.A RNA-directed RNA polymerase
SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors

Seq Identity: 100.00%
Coverage

Model-Template Alignment

Model 03

Structure Assessment

Oligo-State: Monomer

GMQE: 0.86

QMEANDisCo Global:: 0.86 ± 0.05

Ligands

1 x POP, 2 x ZN

1 x PYROPHOSPHATE 2-

POP.3:

3 residues within 4Å:

4 PLIP interactions:

2 x ZINC ION

ZN.1:	4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310
ZN.2:	5 residues within 4Å: Chain A: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646

QMEANDisCo Local

QMEAN Z-Scores

Template

7bv2.1.A RNA-directed RNA polymerase
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)

Seq Identity: 100.00%
Coverage

Ligand	Added to Model	Description
POP	✓	PYROPHOSPHATE 2-
ZN	✓	ZINC ION
ZN	✓	ZINC ION
F86	✕ - Binding site not conserved.	[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate
MG	✕ - Not in contact with model.	MAGNESIUM ION
MG	✕ - Binding site not conserved.	MAGNESIUM ION

Model-Template Alignment

Model 01

Structure Assessment

Oligo-State: Monomer

GMQE: 0.85

QMEANDisCo Global:: 0.89 ± 0.05

Ligands

2 x ZN

QMEANDisCo Local

QMEAN Z-Scores

Template

6nur.1.A NSP12
SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors

Seq Identity: 96.35%
Coverage

Ligand	Added to Model	Description
ZN	✓	ZINC ION
ZN	✓	ZINC ION

Model-Template Alignment

Biounit Oligo State	Hetero-tetramer
QSQE	0.00
Method	EM
Seq Similarity	0.63
Coverage	1.00
Range	31-932

Biounit Oligo State	Hetero-trimer
QSQE	0.00
Method	EM
Seq Similarity	0.63
Coverage	1.00
Range	31-929

Biounit Oligo State	Hetero-tetramer
QSQE	0.00
Method	EM
Seq Similarity	0.61
Coverage	1.00
Range	117-919

RNA-directed RNA polymerase nsp12 (Pol) | P0DTD1 PRO_0000449629

Created: May 5, 2023 at 21:33

Model Results

RNA-directed RNA polymerase nsp12 (Pol) | P0DTD1 PRO_0000449629

Created: May 5, 2023 at 21:33

Model Results

Background

Resolution