Uridylate-specific endoribonuclease nsp15 | P0DTD1 PRO_0000449632

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Uridylate-specific endoribonuclease nsp15 | P0DTD1 PRO_0000449632

Created: Dec. 14, 2022 at 09:35

Structure
Assessment

Oligo-State: Homo-hexamer
(matching prediction)
GMQE: 0.94
QMEANDisCo Global:: 0.87 ± 0.05

Ligands

6 x U5P

QMEANDisCo Local

QMEAN Z-Scores

Template

6wlc.1.A Uridylate-specific endoribonuclease
Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-5'-Monophosphate

Seq Identity: 100.00%
Coverage

Biounit Oligo State	Homo-hexamer
QSQE	0.92
Method	X-ray, 1.82 Å
Seq Similarity	0.61
Coverage	1.00
Range	1-346

Ligand	Added to Model	Description
U5P	✓	URIDINE-5'-MONOPHOSPHATE
U5P	✓	URIDINE-5'-MONOPHOSPHATE
U5P	✓	URIDINE-5'-MONOPHOSPHATE
U5P	✓	URIDINE-5'-MONOPHOSPHATE
U5P	✓	URIDINE-5'-MONOPHOSPHATE
U5P	✓	URIDINE-5'-MONOPHOSPHATE
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
ACT	✕ - Not biologically relevant.	ACETATE ION
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
FMT	✕ - Not biologically relevant.	FORMIC ACID
FMT	✕ - Not in contact with model.	FORMIC ACID
FMT	✕ - Not biologically relevant.	FORMIC ACID
FMT	✕ - Not in contact with model.	FORMIC ACID
FMT	✕ - Not biologically relevant.	FORMIC ACID
FMT	✕ - Not in contact with model.	FORMIC ACID
SO4	✕ - Not biologically relevant.	SULFATE ION
SO4	✕ - Not biologically relevant.	SULFATE ION
SO4	✕ - Not biologically relevant.	SULFATE ION
TRS	✕ - Not biologically relevant.	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRS	✕ - Not biologically relevant.	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRS	✕ - Not biologically relevant.	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRS	✕ - Not biologically relevant.	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRS	✕ - Not biologically relevant.	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRS	✕ - Not biologically relevant.	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Model-Template Alignment

Structure
Assessment

Oligo-State: Homo-hexamer
(matching prediction)
GMQE: 0.94
QMEANDisCo Global:: 0.87 ± 0.05

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

6w01.1.A Uridylate-specific endoribonuclease
The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate

Seq Identity: 100.00%
Coverage

Biounit Oligo State	Homo-hexamer
QSQE	0.92
Method	X-ray, 1.90 Å
Seq Similarity	0.61
Coverage	1.00
Range	1-345

Ligand	Added to Model	Description
CIT	✕ - Not biologically relevant.	CITRIC ACID
CIT	✕ - Not biologically relevant.	CITRIC ACID
CIT	✕ - Not biologically relevant.	CITRIC ACID
CIT	✕ - Not biologically relevant.	CITRIC ACID
CIT	✕ - Not biologically relevant.	CITRIC ACID
CIT	✕ - Not biologically relevant.	CITRIC ACID
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not in contact with model.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER
PEG	✕ - Not biologically relevant.	DI(HYDROXYETHYL)ETHER

Model-Template Alignment

Structure
Assessment

Oligo-State: Homo-hexamer
(matching prediction)
GMQE: 0.92
QMEANDisCo Global:: 0.85 ± 0.05

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

2h85.1.A Putative orf1ab polyprotein
Crystal Structure of Nsp 15 from SARS

Seq Identity: 88.12%
Coverage

Model-Template Alignment

Structure
Assessment

Oligo-State: Homo-hexamer
(matching prediction)
GMQE: 0.91
QMEANDisCo Global:: 0.84 ± 0.05

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

2rhb.1.A Uridylate-specific endoribonuclease
Crystal structure of Nsp15-H234A mutant- Hexamer in asymmetric unit

Seq Identity: 88.44%
Coverage

Model-Template Alignment

U5P.1:	9 residues within 4Å: Chain A: H.249, K.289, V.291, C.292, S.293, Y.342, P.343, K.344, L.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.249, A:S.293, A:S.293, A:S.293, A:L.345
U5P.11:	8 residues within 4Å: Chain B: H.249, K.289, V.291, C.292, S.293, Y.342, K.344, L.345 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.342 Hydrogen bonds: B:H.249, B:S.293, B:S.293, B:S.293, B:L.345
U5P.22:	9 residues within 4Å: Chain C: H.249, K.289, V.291, C.292, S.293, Y.342, P.343, K.344, L.345 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.249, C:S.293, C:S.293, C:S.293, C:L.345
U5P.32:	8 residues within 4Å: Chain D: H.249, K.289, V.291, C.292, S.293, Y.342, K.344, L.345 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.342 Hydrogen bonds: D:H.249, D:S.293, D:S.293, D:S.293, D:L.345
U5P.43:	9 residues within 4Å: Chain E: H.249, K.289, V.291, C.292, S.293, Y.342, P.343, K.344, L.345 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.249, E:S.293, E:S.293, E:S.293, E:L.345
U5P.53:	8 residues within 4Å: Chain F: H.249, K.289, V.291, C.292, S.293, Y.342, K.344, L.345 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Y.342 Hydrogen bonds: F:H.249, F:S.293, F:S.293, F:S.293, F:L.345