nsp7 / nsp8 / Pol hetero-oligomeric complex | P0DTD1 PRO_0000449625, PRO_0000449626, PRO_0000449629

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nsp7 / nsp8 / Pol hetero-oligomeric complex | P0DTD1 PRO_0000449625, PRO_0000449626, PRO_0000449629

Created: May 5, 2023 at 21:33

Model 02

Structure Assessment

Oligo-State: Hetero-1-1-2-mer

GMQE: 0.74

QMEANDisCo Global:: 0.86 ± 0.05

Ligands

2 x ZN

QMEANDisCo Local

QMEAN Z-Scores

Template

6nur.1 NSP7, NSP12, NSP8

Seq Identity: 96.70%
Coverage

Target	Seq Identity	Seq Similarity	Range	Coverage
NSP7	98.80%	0.59	C: 2-71	1.00
NSP12	96.35%	0.61	A: 117-919	1.00
NSP8	97.47%	0.59	BD: 77-191	1.00

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

Model-Template Alignment

Model 01

Structure Assessment

Oligo-State: Hetero-1-1-2-mer

GMQE: 0.72

QMEANDisCo Global:: 0.86 ± 0.05

Ligands

1 x POP, 2 x ZN

1 x PYROPHOSPHATE 2-

POP.5:

7 residues within 4Å:

8 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

7aap.1 Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP

Seq Identity: 100.00%
Coverage

Target	Seq Identity	Seq Similarity	Range	Coverage
Non-structural protein 7	100.00%	0.59	C: 2-68	1.00
Non-structural protein 12	100.00%	0.63	A: 4-929	1.00
Non-structural protein 8	100.00%	0.60	DB: 84-111	1.00

Ligand	Added to Model	Description
POP	✓	PYROPHOSPHATE 2-
ZN	✓	ZINC ION
ZN	✓	ZINC ION
GE6	✕ - Binding site not conserved.	[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
MG	✕ - Not in contact with model.	MAGNESIUM ION
MG	✕ - Not in contact with model.	MAGNESIUM ION
MG	✕ - Not in contact with model.	MAGNESIUM ION

Model-Template Alignment

Biounit Oligo State	Hetero-tetramer
QSQE	-
Method	EM
Overall Seq Identity	96.70%
Overall Seq Similarity	0.61

Biounit Oligo State	Hetero-tetramer
QSQE	0.68
Method	EM
Overall Seq Identity	100.00%
Overall Seq Similarity	0.62

nsp7 / nsp8 / Pol hetero-oligomeric complex | P0DTD1 PRO_0000449625, PRO_0000449626, PRO_0000449629

Created: May 5, 2023 at 21:33

Model Results

Background

Resolution