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1MT1-A-D

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

Protein

Peptide
Chain D 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) 11864
ASA (protein) 7397
ASA (peptide) 4837
BProA 174
BPepA 196
BPP% 4%
BSA 185

Interaction energy (calculated using Prodigy)

Intermolecular contacts 11
Charged-charged 0
Charged-polar 0
Charged-apolar 0
Polar-polar 0
Apolar-polar 1
Apolar-apolar 10
Apolar NIS residues 53.57%
Charged NIS residues 24.29%
Predicted free energy of binding (kcal/mol) -2.8
Predicted dissociation constant (M, 25 ˚C) 0.0087

Interface properties (calculated using PISA)

Interface significance
Interface evidence moderate
Complexation significance score (CSS) 0.069
Surface area
Interface area (Ų) 183
Buried area (peptide, Ų) 195
Buried area (protein, Ų) 171
Total buried area (Ų) 666
Complex ASA (Ų) 11901
Dissociation area (Ų) 183
Energy (predicted)
Dissociation free energy ΔGdiss (kcal/mol) -5.206
Solvation energy gain ΔiG (kcal/mol) -4.25
ΔiG P-value 0.227
Solvation energy (peptide, kcal/mol) -2.501
Solvation energy (protein, kcal/mol) -1.749
Total interaction energy ΔiG (kcal/mol) -4.305
Dissociation entropy TΔS (kcal/mol) 9.901
Contacts
Hydrogen bonds 1
Salt bridges 0
Interface residues (peptide) 5
Interface atoms (peptide) 14
Interface residues (protein) 6
Interface atoms (protein) 19

Interface residues

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Contacts (calculated using COCaDA)

Filter:
Contact Chain1 R1 Atom1 Chain2 R2 Atom2 Distance Local Type Show
F12/W163 A F12 CZ D W163 CH2 4.38 INTER HY
L14/P68 A L14 CD2 D P68 CB 3.98 INTER HY
P15/L72 A P15 CG D L72 CG 4.45 INTER HY
P15/L72 A P15 CG D L72 CD1 4.12 INTER HY
P15/L72 A P15 CG D L72 CD2 4.4 INTER HY
I51/L72 A I51 CD1 D L72 CD2 4.24 INTER HY
S52/Y77 A S52 OG D Y77 OH 2.63 INTER HB
30%

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