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1MT1-A-F

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: F
Protein length: 110
Description: The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii
Organism: METHANOCALDOCOCCUS JANNASCHII

Protein

Peptide
Chain F 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) 11271
ASA (protein) 7244
ASA (peptide) 4837
BProA 388
BPepA 423
BPP% 9%
BSA 405

Interaction energy (calculated using Prodigy)

Intermolecular contacts 32
Charged-charged 3
Charged-polar 2
Charged-apolar 7
Polar-polar 1
Apolar-polar 12
Apolar-apolar 7
Apolar NIS residues 53.57%
Charged NIS residues 24.29%
Predicted free energy of binding (kcal/mol) -6.1
Predicted dissociation constant (M, 25 ˚C) 3.4e-05

Interface properties (calculated using PISA)

Interface significance
Interface evidence strong
Complexation significance score (CSS) 1.000
Surface area
Interface area (Ų) 404
Buried area (peptide, Ų) 421
Buried area (protein, Ų) 388
Total buried area (Ų) 1338
Complex ASA (Ų) 11082
Dissociation area (Ų) 522
Energy (predicted)
Dissociation free energy ΔGdiss (kcal/mol) -4.357
Solvation energy gain ΔiG (kcal/mol) -2.853
ΔiG P-value 0.516
Solvation energy (peptide, kcal/mol) 0.517
Solvation energy (protein, kcal/mol) -3.37
Total interaction energy ΔiG (kcal/mol) -2.196
Dissociation entropy TΔS (kcal/mol) 10.169
Contacts
Hydrogen bonds 4
Salt bridges 4
Interface residues (peptide) 11
Interface atoms (peptide) 35
Interface residues (protein) 16
Interface atoms (protein) 46

Interface residues

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Contacts (calculated using COCaDA)

Filter:
Contact Chain1 R1 Atom1 Chain2 R2 Atom2 Distance Local Type Show
E28/E125 A E28 OE2 F E125 OE2 5.5 INTER RE
E28/I129 A E28 CB F I129 CD1 4.06 INTER HY
E28/I129 A E28 CG F I129 CD1 4.39 INTER HY
E28/E132 A E28 OE1 F E132 OE1 5.31 INTER RE
N32/I129 A N32 CB F I129 CG2 4.18 INTER HY
D35/R134 A D35 OD1 F R134 CZ 3.76 INTER SB
D35/R134 A D35 OD1 F R134 NH1 3.76 INTER HB
D35/R134 A D35 OD1 F R134 NH2 2.89 INTER HB
D35/R134 A D35 OD2 F R134 NH1 2.83 INTER HB
D35/R134 A D35 OD2 F R134 NH2 3.48 INTER HB
L39/R134 A L39 CD1 F R134 CG 4.12 INTER HY
L39/R134 A L39 CD2 F R134 CG 4.27 INTER HY
G44/R134 A G44 O F R134 NH2 3.04 INTER HB
N45/R134 A N45 OD1 F R134 NE 2.79 INTER HB
N45/R134 A N45 OD1 F R134 NH2 3.26 INTER HB
N47/I54 A N47 OD1 F I54 N 2.74 INTER HB
N47/I54 A N47 ND2 F I54 O 2.78 INTER HB
30%

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