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1MT1-A-B

PDB UniProt PubMed
PDB ID: 1MT1
Structure method: X-RAY DIFFRACTION
Resolution: 2.2
Multipro: 1MT1-A
Peptide chain: A
Peptide length: 47
Protein chain: B
Protein length: 110
Description: The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii
Organism: METHANOCALDOCOCCUS JANNASCHII

Protein

Peptide
Chain B A
Description PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN
Length (residues) 110 47
Molecular Weight (Da) 11557.28 4752.339
Isoelectric Point (pI) 5.21 5.454
Instability Index 25.51 10.891
Aliphatic Index 101.31 114.565
GRAVY 0.05 0.326
Hydrophobic (%) 44.86 45.652
Positive Residues 13 2
Negative Residues 16 3
Atomic Formula C527H838N130O153S3 C214H339N57O64
Total Atoms 1651 674
Extinction Coeff. (with disulfide) 17147 1490
Extinction Coeff. (no disulfide) 17335 1490
Sequence 
XIXPPEAEIVPLPKLPXGALVPTAYGYIISDVPGETISAA
ISVAIPKDKSLCGLIEYEGKCSKKEAEKTVREAKIGFERG
WELDRIESIAVEHTVEKLGCAFAAAALWYK
 
PLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNV
NLIRISX

Classifications

Structural similiarities

Cluster leader
Similar complex 1MT1-A-B
Similar peptide 1MT1-A-B
PDB classification LYASE

Therapeutic classes

Anti-Angiogenic (AAP) ❌
Antibacterial (ABP) ❌
Anticancer (ACP) ❌
Anti-Inflammatory (AIP) ❌
Quorum Sensing (QSP) ❌
Surface Binding (SBP) ❌

Propedia v1 classes

Binding site -
Interface -
Sequence -

Protein-peptide interactions

Surface (calculated using Naccess)

ASA (complex) 8637
ASA (protein) 7280
ASA (peptide) 4837
BProA 1612
BPepA 1868
BPP% 39%
BSA 1740

Interaction energy (calculated using Prodigy)

Intermolecular contacts 189
Charged-charged 6
Charged-polar 11
Charged-apolar 16
Polar-polar 1
Apolar-polar 49
Apolar-apolar 106
Apolar NIS residues 50.81%
Charged NIS residues 27.42%
Predicted free energy of binding (kcal/mol) -15.7
Predicted dissociation constant (M, 25 ˚C) 2.8e-12

Interface properties (calculated using PISA)

Interface significance
Interface evidence strong
Complexation significance score (CSS) 0.995
Surface area
Interface area (Ų) 1735
Buried area (peptide, Ų) 1862
Buried area (protein, Ų) 1607
Total buried area (Ų) 3768
Complex ASA (Ų) 8667
Dissociation area (Ų) 1735
Energy (predicted)
Dissociation free energy ΔGdiss (kcal/mol) 28.005
Solvation energy gain ΔiG (kcal/mol) -25.844
ΔiG P-value 0.276
Solvation energy (peptide, kcal/mol) -12.029
Solvation energy (protein, kcal/mol) -13.816
Total interaction energy ΔiG (kcal/mol) -25.898
Dissociation entropy TΔS (kcal/mol) 10.573
Contacts
Hydrogen bonds 27
Salt bridges 2
Interface residues (peptide) 33
Interface atoms (peptide) 153
Interface residues (protein) 51
Interface atoms (protein) 190

Interface residues

Click a residue to show it in the 3D viewer.

Contacts (calculated using COCaDA)

Filter:
Contact Chain1 R1 Atom1 Chain2 R2 Atom2 Distance Local Type Show
K13/Y164 A K13 CG B Y164 CD1 4.02 INTER HY
K13/Y164 A K13 CG B Y164 CE1 4.26 INTER HY
K13/Y164 A K13 CD B Y164 CD1 4.32 INTER HY
L14/P56 A L14 CB B P56 CB 4.33 INTER HY
L14/P56 A L14 CB B P56 CG 4.47 INTER HY
L14/P56 A L14 CD2 B P56 CB 4.37 INTER HY
P15/P56 A P15 CB B P56 CG 4.38 INTER HY
P15/L162 A P15 CB B L162 CB 3.74 INTER HY
P15/L162 A P15 CB B L162 CG 4.27 INTER HY
P15/L162 A P15 CB B L162 CD2 4.26 INTER HY
P15/L162 A P15 CG B L162 CB 4.1 INTER HY
P15/L162 A P15 CG B L162 CD2 4.3 INTER HY
P15/Y164 A P15 CB B Y164 CE1 4.4 INTER HY
P15/Y164 A P15 CG B Y164 CE1 4.09 INTER HY
P15/Y164 A P15 CG B Y164 CE2 4.39 INTER HY
N16/E60 A N16 O B E60 N 2.97 INTER HB
N16/W163 A N16 N B W163 O 2.94 INTER HB
N16/K165 A N16 OD1 B K165 N 2.65 INTER HB
T17/V62 A T17 CG2 B V62 CG1 4.49 INTER HY
T17/V62 A T17 CG2 B V62 CG2 4.02 INTER HY
T17/W163 A T17 N B W163 O 3.2 INTER HB
T17/W163 A T17 O B W163 N 2.94 INTER HB
T17/W163 A T17 OG1 B W163 N 3.47 INTER HB
T17/W163 A T17 OG1 B W163 O 3.24 INTER HB
T17/Y164 A T17 OG1 B Y164 N 3.82 INTER HB
T17/K165 A T17 CG2 B K165 CB 3.48 INTER HY
T17/K165 A T17 CG2 B K165 CG 4.33 INTER HY
V18/E60 A V18 N B E60 O 2.96 INTER HB
V18/I61 A V18 CB B I61 CG1 4.5 INTER HY
V18/V62 A V18 O B V62 N 2.95 INTER HB
V18/A160 A V18 CG1 B A160 CB 4.05 INTER HY
V18/L162 A V18 CG1 B L162 CD1 4.44 INTER HY
V18/L162 A V18 CG2 B L162 CG 4.09 INTER HY
V18/L162 A V18 CG2 B L162 CD1 4.15 INTER HY
S19/V62 A S19 OG B V62 O 2.96 INTER HB
S19/P63 A S19 OG B P63 O 3.63 INTER HB
S19/L64 A S19 OG B L64 N 3.44 INTER HB
S19/A161 A S19 N B A161 O 2.84 INTER HB
S19/A161 A S19 O B A161 N 2.78 INTER HB
L20/I93 A L20 CD2 B I93 CG2 3.54 INTER HY
L20/V95 A L20 CD2 B V95 CG2 3.77 INTER HY
L20/E142 A L20 CD1 B E142 CB 4.31 INTER HY
L20/I144 A L20 CB B I144 CB 4.29 INTER HY
L20/I144 A L20 CB B I144 CG2 3.95 INTER HY
L20/A160 A L20 CD2 B A160 CB 3.74 INTER HY
V21/L64 A V21 CG1 B L64 CB 4.17 INTER HY
V21/L64 A V21 CG1 B L64 CG 4.32 INTER HY
V21/L64 A V21 CG1 B L64 CD1 4.27 INTER HY
V21/L64 A V21 CG1 B L64 CD2 3.82 INTER HY
V21/A159 A V21 N B A159 O 2.91 INTER HB
V21/A159 A V21 O B A159 N 2.79 INTER HB
V21/A159 A V21 CG2 B A159 CB 4.08 INTER HY
A22/I144 A A22 CB B I144 CG1 3.95 INTER HY
A22/I144 A A22 CB B I144 CG2 4.41 INTER HY
A22/I144 A A22 CB B I144 CD1 3.69 INTER HY
A22/V146 A A22 CB B V146 CB 3.87 INTER HY
A22/V146 A A22 CB B V146 CG1 3.95 INTER HY
A22/A158 A A22 CB B A158 CB 4.3 INTER HY
G23/F157 A G23 N B F157 O 2.8 INTER HB
G23/F157 A G23 O B F157 N 2.79 INTER HB
S24/H148 A S24 OG B H148 ND1 3.19 INTER HB
S25/H148 A S25 O B H148 NE2 3.89 INTER HB
S25/C155 A S25 N B C155 O 2.99 INTER HB
S25/C155 A S25 O B C155 N 2.84 INTER HB
E26/H148 A E26 OE1 B H148 NE2 3.09 INTER uSB
E26/H148 A E26 OE1 B H148 NE2 3.09 INTER HB
E26/E151 A E26 OE1 B E151 N 3.36 INTER HB
E26/E151 A E26 OE1 B E151 OE1 5.07 INTER RE
E26/E151 A E26 OE2 B E151 N 3.45 INTER HB
E26/K152 A E26 OE2 B K152 N 2.56 INTER HB
E26/L153 A E26 OE2 B L153 N 2.62 INTER HB
G27/L153 A G27 N B L153 O 2.94 INTER HB
P30/I81 A P30 CB B I81 CG2 4.32 INTER HY
P30/I81 A P30 CB B I81 CD1 3.89 INTER HY
A33/L153 A A33 CB B L153 CD2 3.84 INTER HY
A33/C155 A A33 CB B C155 CB 4.0 INTER HY
F34/Y77 A F34 CE1 B Y77 CE1 4.3 INTER HY
F34/Y77 A F34 CZ B Y77 CE1 4.17 INTER HY
F34/Y79 A F34 CD1 B Y79 CB 4.38 INTER HY
F34/Y79 A F34 CD1 B Y79 CG 4.12 INTER HY
F34/Y79 A F34 CD1 B Y79 CD1 3.9 INTER HY
F34/Y79 A F34 CD1 B Y79 CE1 4.42 INTER HY
F34/Y79 A F34 CE1 B Y79 CB 4.12 INTER HY
F34/Y79 A F34 CE1 B Y79 CG 3.89 INTER HY
F34/Y79 A F34 CE1 B Y79 CD1 4.1 INTER HY
F34/Y79 A F34 CE1 B Y79 CD2 4.24 INTER HY
F34/F157 A F34 CE1 B F157 CD1 3.86 INTER HY
F34/F157 A F34 CE1 B F157 CE1 4.15 INTER HY
F34/F157 A F34 CZ B F157 CD1 4.42 INTER HY
F34/F157 A F34 CZ B F157 CE1 4.28 INTER HY
A37/C155 A A37 CB B C155 CB 4.34 INTER HY
A37/F157 A A37 CB B F157 CB 3.82 INTER HY
L38/F157 A L38 CD2 B F157 CG 3.99 INTER HY
L38/F157 A L38 CD2 B F157 CD1 3.78 INTER HY
L38/F157 A L38 CD2 B F157 CD2 3.86 INTER HY
L38/F157 A L38 CD2 B F157 CE1 3.42 INTER HY
L38/F157 A L38 CD2 B F157 CE2 3.51 INTER HY
L38/F157 A L38 CD2 B F157 CZ 3.28 INTER HY
A41/F157 A A41 CB B F157 CD2 4.14 INTER HY
A41/F157 A A41 CB B F157 CE2 4.19 INTER HY
I43/L64 A I43 CG2 B L64 CG 4.23 INTER HY
I43/L64 A I43 CG2 B L64 CD1 3.87 INTER HY
I43/L64 A I43 CG2 B L64 CD2 3.4 INTER HY
I43/L64 A I43 CD1 B L64 CD1 4.43 INTER HY
I43/L67 A I43 CG1 B L67 CD1 4.08 INTER HY
I43/L67 A I43 CG2 B L67 CD1 4.36 INTER HY
I43/L67 A I43 CD1 B L67 CD1 4.2 INTER HY
I43/F157 A I43 CG1 B F157 CE2 4.31 INTER HY
I43/F157 A I43 CG2 B F157 CE2 4.31 INTER HY
I43/F157 A I43 CD1 B F157 CE2 3.62 INTER HY
I43/F157 A I43 CD1 B F157 CZ 3.73 INTER HY
I43/A159 A I43 CD1 B A159 CB 4.47 INTER HY
I43/A161 A I43 CD1 B A161 CB 3.86 INTER HY
N45/G70 A N45 O B G70 N 2.88 INTER HB
V46/L67 A V46 CG1 B L67 CB 3.79 INTER HY
V46/L67 A V46 CG1 B L67 CD1 4.17 INTER HY
V46/L67 A V46 CG2 B L67 CD1 4.44 INTER HY
V46/V73 A V46 CB B V73 CG2 4.18 INTER HY
V46/V73 A V46 CG2 B V73 CG2 4.13 INTER HY
N47/G70 A N47 ND2 B G70 O 2.94 INTER HB
N47/A71 A N47 N B A71 O 2.73 INTER HB
N47/L72 A N47 CB B L72 CD2 3.64 INTER HY
N47/V73 A N47 O B V73 N 2.77 INTER HB
L48/T75 A L48 CB B T75 CG2 3.29 INTER HY
L48/T75 A L48 CG B T75 CG2 3.79 INTER HY
L48/T75 A L48 CD1 B T75 CG2 3.96 INTER HY
L48/T75 A L48 CD2 B T75 CG2 4.27 INTER HY
L48/T75 A L48 CD2 B T75 CG2 3.55 INTER HY
L48/Y77 A L48 CB B Y77 CE2 4.34 INTER HY
L48/Y77 A L48 CD1 B Y77 CD2 4.14 INTER HY
L48/Y77 A L48 CD1 B Y77 CE2 4.07 INTER HY
L48/F157 A L48 CD1 B F157 CE1 4.3 INTER HY
L48/F157 A L48 CD1 B F157 CZ 3.99 INTER HY
I49/L72 A I49 CG1 B L72 CB 4.0 INTER HY
I49/L72 A I49 CD1 B L72 CB 4.24 INTER HY
I49/V73 A I49 N B V73 O 2.87 INTER HB
I49/T75 A I49 O B T75 N 2.91 INTER HB
I49/T75 A I49 O B T75 N 2.92 INTER HB
R50/Y77 A R50 CB B Y77 CD2 4.46 INTER HY
R50/Y77 A R50 CB B Y77 CE2 3.72 INTER HY
R50/Y77 A R50 CG B Y77 CD2 4.05 INTER HY
R50/Y77 A R50 CG B Y77 CE1 4.46 INTER HY
R50/Y77 A R50 CG B Y77 CE2 3.65 INTER HY
R50/Y77 A R50 NE B Y77 O 3.62 INTER HB
R50/Y77 A R50 NH2 B Y77 O 2.89 INTER HB
R50/E109 A R50 NH2 B E109 OE1 3.1 INTER SB
R50/E109 A R50 NH2 B E109 OE1 3.1 INTER HB
R50/E111 A R50 NH2 B E111 OE1 5.08 INTER AT
I51/P74 A I51 CG1 B P74 CB 4.17 INTER HY
I51/P74 A I51 CG2 B P74 CB 4.16 INTER HY
I51/P74 A I51 CD1 B P74 CB 3.66 INTER HY
I51/T75 A I51 N B T75 O 2.94 INTER HB
I51/T75 A I51 N B T75 O 2.89 INTER HB
I51/T75 A I51 N B T75 O 2.94 INTER HB
I51/T75 A I51 N B T75 O 2.89 INTER HB
I51/A76 A I51 CG1 B A76 CB 3.67 INTER HY
I51/A76 A I51 CD1 B A76 CB 3.89 INTER HY
I51/L162 A I51 CD1 B L162 CD2 3.85 INTER HY
I51/L162 A I51 CD1 B L162 CD1 4.05 INTER HY
I51/L162 A I51 CD1 B L162 CD2 4.0 INTER HY
30%

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