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

Background |  |  |

3D Viewer
NGL PV

### 4_1_Oct_SF_Bin32_scaffold_7496_c1_2-2440_1

### Created: March 29, 2023, 8:38 p.m. at 20:38

Order by:

Oligo-State
  Monomer
GMQE
  0.70
QMEANDisCo Global:
  0.67 ± 0.05

Ligands
  1 x MO
  1 x MOLYBDENUM ATOM

  MO.7: | 4 residues within 4Å: Chain B: H.102, D.104, G.409, K.764 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
  40.77%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.97 Å
Seq Similarity | 0.41
Coverage | 0.95
Range | 1-811

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
  0.37
QMEANDisCo Global:
  0.51 ± 0.05

Ligands

QMEANDisCo Local
QMEAN Z-Scores

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

Seq Identity
  23.32%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.30 Å
Seq Similarity | 0.32
Coverage | 0.62
Range | 1-588

Ligand | Added to Model | Description
--- | --- | ---
6MO | ✕ - Not in contact with model. | 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
  0.20
QMEANDisCo Global:
  0.46 ± 0.05

Ligands

QMEANDisCo Local
QMEAN Z-Scores

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

Seq Identity
  31.10%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | X-ray, 2.50 Å
Seq Similarity | 0.36
Coverage | 0.42
Range | 90-451

Ligand | Added to Model | Description
--- | --- | ---
6MO | ✕ - Binding site not conserved. | 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
  0.04
QMEANDisCo Global:
  0.42 ± 0.08

Ligands

QMEANDisCo Local
QMEAN Z-Scores

Template
1r27.4.A Respiratory nitrate reductase 1 alpha chain
Crystal Structure of NarGH complex

Seq Identity
  17.24%
Coverage

Biounit Oligo State | Hetero-octamer
QSQE | 0.00
Method | X-ray, 2.00 Å
Seq Similarity | 0.27
Coverage | 0.14
Range | 654-769

Ligand | Added to Model | Description
--- | --- | ---
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
F3S | ✕ - Binding site not conserved. | FE3-S4 CLUSTER
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
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
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
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
MO | ✕ - Binding site not conserved. | MOLYBDENUM ATOM
MO | ✕ - Binding site not conserved. | MOLYBDENUM ATOM
MO | ✕ - Binding site not conserved. | MOLYBDENUM ATOM
MO | ✕ - Binding site not conserved. | MOLYBDENUM ATOM
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
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
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
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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