Export Alignment
Secondary Structure
None DSSP PSIPRED SSpro
Colour Scheme
Fade Mismatches Enhance Mismatches
Confidencegradient Confidenceclass Indels Chain Unique Chain Rainbow 2° Structure Clustal Hydrophobic Size Charged Polar Proline Ser/Thr Cysteine Aliphatic Aromatic No Colour
Use QMEANBrane values

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NGL PV

### 4_1_May_SF_Bin52_scaffold_5716_c1_3776-6595_1

### Created: March 29, 2023, 8:37 p.m. at 20:37

Order by:

Oligo-State
  Monomer
GMQE
  0.68
QMEANDisCo Global:
  0.69 ± 0.05

Ligands
  1 x MO
  1 x MOLYBDENUM ATOM

  MO.7: | 3 residues within 4Å: Chain B: H.281, D.283, G.588 Ligand excluded by PLIP

QMEANDisCo Local
QMEAN Z-Scores

Template
7b04.1.B Nitrite oxidoreductase subunit A
Structure of Nitrite oxidoreductase (Nxr) from the anammox bacterium Kuenenia stuttgartiensis.

Seq Identity
  39.66%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.97 Å
Seq Similarity | 0.40
Coverage | 0.95
Range | 29-938

Ligand | Added to Model | Description
--- | --- | ---
MO | ✓ | MOLYBDENUM ATOM
CA | ✕ - Binding site not conserved. | CALCIUM ION
CA | ✕ - Binding site not conserved. | CALCIUM ION
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
HEM | ✕ - Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.67
QMEANDisCo Global:
  0.68 ± 0.05

Ligands
  1 x MO
  1 x MOLYBDENUM ATOM

  MO.7: | 3 residues within 4Å: Chain B: H.281, D.283, G.588 Ligand excluded by PLIP

QMEANDisCo Local
QMEAN Z-Scores

Template
7b04.1.B Nitrite oxidoreductase subunit A
Structure of Nitrite oxidoreductase (Nxr) from the anammox bacterium Kuenenia stuttgartiensis.

Seq Identity
  41.29%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.97 Å
Seq Similarity | 0.41
Coverage | 0.91
Range | 47-938

Ligand | Added to Model | Description
--- | --- | ---
MO | ✓ | MOLYBDENUM ATOM
CA | ✕ - Binding site not conserved. | CALCIUM ION
CA | ✕ - Binding site not conserved. | CALCIUM ION
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
HEM | ✕ - Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.40
QMEANDisCo Global:
  0.54 ± 0.05

Ligands
  1 x 6MO
  1 x MOLYBDENUM(VI) ION

  6MO.3: | 3 residues within 4Å: Chain A: N.78, D.283, G.588 No protein-ligand interaction detected (PLIP)

QMEANDisCo Local
QMEAN Z-Scores

Template
3ir5.1.A Respiratory nitrate reductase 1 alpha chain
Crystal structure of NarGHI mutant NarG-H49C

Seq Identity
  25.36%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.30 Å
Seq Similarity | 0.33
Coverage | 0.67
Range | 54-767

Ligand | Added to Model | Description
--- | --- | ---
6MO | ✓ | MOLYBDENUM(VI) ION
AGA | ✕ - Binding site not conserved. | (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
HEM | ✕ - Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
HEM | ✕ - Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.37
QMEANDisCo Global:
  0.48 ± 0.05

Ligands

QMEANDisCo Local
QMEAN Z-Scores

Template
6sdv.1.A Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form

Seq Identity
  18.11%
Coverage

Biounit Oligo State | Hetero-dimer
QSQE | 0.00
Method | X-ray, 1.90 Å
Seq Similarity | 0.29
Coverage | 0.64
Range | 54-767

Ligand | Added to Model | Description
--- | --- | ---
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
GOL | ✕ - Not biologically relevant. | GLYCEROL
H2S | ✕ - Binding site not conserved. | HYDROSULFURIC ACID
MGD | ✕ - Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD | ✕ - Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
NO3 | ✕ - Not biologically relevant. | NITRATE ION
NO3 | ✕ - Not biologically relevant. | NITRATE ION
PEG | ✕ - Not biologically relevant. | DI(HYDROXYETHYL)ETHER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
W | ✕ - Not in contact with model. | TUNGSTEN ION

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.26
QMEANDisCo Global:
  0.45 ± 0.05

Ligands
  1 x 6MO
  1 x MOLYBDENUM(VI) ION

  6MO.4: | 5 residues within 4Å: Chain A: N.78, A.279, W.280, D.283, G.588 No protein-ligand interaction detected (PLIP)

QMEANDisCo Local
QMEAN Z-Scores

Template
3ir7.1.A Respiratory nitrate reductase 1 alpha chain
Crystal structure of NarGHI mutant NarG-R94S

Seq Identity
  31.57%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.50 Å
Seq Similarity | 0.36
Coverage | 0.54
Range | 54-630

Ligand | Added to Model | Description
--- | --- | ---
6MO | ✓ | MOLYBDENUM(VI) ION
AGA | ✕ - Binding site not conserved. | (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
HEM | ✕ - Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
HEM | ✕ - Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1 | ✕ - Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER
SF4 | ✕ - Binding site not conserved. | IRON/SULFUR CLUSTER

Model-Template Alignment

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