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1WRZ-B-A

PDB UniProt PubMed
PDB ID: 1WRZ
Structure method: X-RAY DIFFRACTION
Resolution: 2.0
Complex: 1WRZ-B
Peptide chain: B
Peptide length: 19
Protein chain: A
Protein length: 147
Description: Calmodulin complexed with a peptide from a human death-associated protein kinase
Organism: HOMO SAPIENS

Protein

Peptide
Chain A B
Description calmodulin Death-associated protein kinase 2
Length (residues) 147 19
Molecular Weight (Da) 16635.15 2372.796
Isoelectric Point (pI) 4.09 12.0
Instability Index 28.19 90.979
Aliphatic Index 65.71 97.368
GRAVY -0.69 -0.379
Hydrophobic (%) 36.05 36.842
Positive Residues 14 5
Negative Residues 38 0
Atomic Formula C711H1113N187O253S9 C105H172N36O24S1
Total Atoms 2273 338
Extinction Coeff. (with disulfide) 2980 5562
Extinction Coeff. (no disulfide) 2980 5625
Sequence 
DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQ
NPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDS
EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEV
DEMIREADIDGDGQVNYEEFVQMMTAK
 
RRRWKLSFSIVSLCNHLTR

Classifications

Structural similiarities

  • Unique complex :
  • Similar complex : 1WRZ-B-A
  • Similar peptide : 1WRZ-B-A
  • PDB classification : METAL BINDING PROTEIN/TRANSFERASE

Therapeutic classes

  • Anti-Angiogenic (AAP) : ❌ 0.45
  • Antibacterial (ABP) : ✅ 1.0
  • Anticancer (ACP) : ✅ 0.92
  • Anti-Inflammatory (AIP) : ❌ 0.13
  • Quorum Sensing (QSP) : ✅ 1.0
  • Surface Binding (SBP) : ❌ 0.12

Propedia v1 classes

  • Binding site : -
  • Interface : -
  • Sequence : -

Protein-peptide interactions

Surface (calculated using Naccess)

  • ASA (complex): 9068
  • ASA (protein) : 9776
  • ASA (peptide) : 2419
  • BProA : 1440
  • BPepA : 1687
  • BPP% : 70%
  • BSA : 1564

Interaction energy (calculated using Prodigy)

  • Number of intermolecular contacts : 134
  • Number of charged-charged contacts : 25
  • Number of charged-polar contacts : 7
  • Number of charged-apolar contacts : 25
  • Number of polar-polar contacts : 2
  • Number of apolar-polar contacts : 19
  • Number of apolar-apolar contacts : 56
  • Percentage of apolar NIS residues : 30.0%
  • Percentage of charged NIS residues : 43.08%
  • Predicted binding affinity (kcal/mol) : -13.2
  • Predicted dissociation constant (M) at 25.0˚C : 2.2e-10

Interface residues


7, 10, 11, 12, 14, 15, 16, 18, 19, 32, 35, 36, 39, 41, 43, 47, 51, 54, 68, 71, 72, 75, 76, 77, 78, 79, 80, 84, 85, 87, 88, 89, 91, 92, 100, 105, 108, 109, 112, 114, 116, 120, 123, 124, 125, 127, 128, 136, 141, 143, 144, 145, 146, 147, 148

Contacts (calculated using COCaDA)

Filter results:
Only side chain contacts
Contact Chain1 R1 Atom1 Chain2 R2 Atom2 Distance Local Type Show
E7/R303 A E7 OE1 B R303 NE 2.71 INTER SB
E7/R303 A E7 OE1 B R303 NE 2.71 INTER HB
E7/R303 A E7 OE1 B R303 NH2 3.43 INTER HB
E7/R303 A E7 OE1 B R303 NE 3.72 INTER HB
E7/R303 A E7 OE1 B R303 NH2 2.94 INTER HB
E7/R303 A E7 OE2 B R303 NE 2.87 INTER HB
E7/R303 A E7 OE2 B R303 NH2 3.58 INTER HB
E7/K306 A E7 OE1 B K306 NZ 5.67 INTER AT
A10/R303 A A10 O B R303 NH1 3.48 INTER HB
E11/R303 A E11 CG B R303 CG 3.44 INTER HY
E11/R303 A E11 OE1 B R303 NE 4.91 INTER AT
E11/K306 A E11 OE1 B K306 NZ 3.11 INTER SB
E11/K306 A E11 OE1 B K306 NZ 3.11 INTER HB
E11/K306 A E11 OE2 B K306 NZ 3.8 INTER HB
E14/R303 A E14 OE1 B R303 NH1 3.1 INTER SB
E14/R303 A E14 OE1 B R303 NH1 3.1 INTER HB
E14/L307 A E14 CG B L307 CG 4.41 INTER HY
E14/L307 A E14 CG B L307 CD1 4.39 INTER HY
A15/L307 A A15 CB B L307 CD2 3.89 INTER HY
A15/I311 A A15 CB B I311 CG1 4.24 INTER HY
A15/I311 A A15 CB B I311 CD1 3.89 INTER HY
L18/L307 A L18 CD1 B L307 CD1 3.94 INTER HY
L18/I311 A L18 CB B I311 CD1 4.41 INTER HY
L18/I311 A L18 CG B I311 CD1 4.26 INTER HY
L18/I311 A L18 CD1 B I311 CD1 3.15 INTER HY
F19/I311 A F19 CE2 B I311 CG1 4.23 INTER HY
F19/I311 A F19 CE2 B I311 CG2 4.08 INTER HY
F19/I311 A F19 CZ B I311 CG2 3.93 INTER HY
F19/L314 A F19 CE2 B L314 CD2 4.33 INTER HY
F19/L314 A F19 CZ B L314 CD2 4.06 INTER HY
L32/L318 A L32 CD1 B L318 CD1 4.43 INTER HY
V35/I311 A V35 CG1 B I311 CG2 4.29 INTER HY
M36/C315 A M36 CG B C315 CB 4.39 INTER HY
M36/L318 A M36 CE B L318 CB 3.68 INTER HY
M36/L318 A M36 CE B L318 CG 4.1 INTER HY
M36/L318 A M36 CE B L318 CD1 3.26 INTER HY
L39/V312 A L39 CD1 B V312 CG2 4.15 INTER HY
L39/V312 A L39 CD2 B V312 CG2 4.47 INTER HY
L39/C315 A L39 CD1 B C315 CB 4.05 INTER HY
Q41/C315 A Q41 NE2 B C315 O 3.77 INTER HB
Q41/T319 A Q41 CB B T319 CG2 4.42 INTER HY
Q41/T319 A Q41 CG B T319 CG2 4.46 INTER HY
Q41/T319 A Q41 OE1 B T319 OG1 3.7 INTER HB
Q41/T319 A Q41 NE2 B T319 OG1 2.41 INTER HB
M51/L318 A M51 CB B L318 CD2 4.37 INTER HY
M51/L318 A M51 CG B L318 CB 4.2 INTER HY
M51/L318 A M51 CG B L318 CD2 4.1 INTER HY
M51/L318 A M51 CE B L318 CB 4.35 INTER HY
M51/T319 A M51 CE B T319 CG2 4.35 INTER HY
E54/R320 A E54 OE1 B R320 NH1 5.63 INTER AT
F68/L314 A F68 CE1 B L314 CD2 4.37 INTER HY
M71/L314 A M71 CG B L314 CD1 4.3 INTER HY
K75/L314 A K75 CB B L314 CD1 3.49 INTER HY
K75/L314 A K75 CG B L314 CD1 4.47 INTER HY
K75/H317 A K75 O B H317 ND1 3.33 INTER HB
K75/H317 A K75 CB B H317 CB 4.44 INTER HY
K75/L318 A K75 CB B L318 CD2 4.4 INTER HY
K75/L318 A K75 CG B L318 CG 4.29 INTER HY
K75/L318 A K75 CG B L318 CD2 3.52 INTER HY
K75/R320 A K75 NZ B R320 NE 5.28 INTER RE
M76/S310 A M76 SD B S310 OG 3.61 INTER HB
M76/S313 A M76 SD B S313 OG 3.55 INTER HB
M76/L314 A M76 CB B L314 CB 4.42 INTER HY
M76/L314 A M76 CB B L314 CD1 4.16 INTER HY
M76/L314 A M76 CG B L314 CB 3.92 INTER HY
T79/H317 A T79 O B H317 NE2 3.56 INTER HB
D80/H317 A D80 N B H317 NE2 3.49 INTER HB
D80/H317 A D80 OD2 B H317 NE2 3.73 INTER uSB
D80/H317 A D80 OD2 B H317 NE2 3.73 INTER HB
E84/H317 A E84 OE1 B H317 NE2 5.35 INTER uAT
I85/F309 A I85 CG1 B F309 CE1 4.47 INTER HY
I85/F309 A I85 CG1 B F309 CZ 4.28 INTER HY
A88/F309 A A88 CB B F309 CD1 4.32 INTER HY
A88/F309 A A88 CB B F309 CE1 4.07 INTER HY
A88/V312 A A88 CB B V312 CG1 3.81 INTER HY
V91/V312 A V91 CB B V312 CG1 4.02 INTER HY
V91/V312 A V91 CG1 B V312 CG1 4.39 INTER HY
V91/V312 A V91 CG1 B V312 CG2 4.32 INTER HY
V91/V312 A V91 CG2 B V312 CG1 3.7 INTER HY
F92/W305 A F92 CD1 B W305 CZ3 4.09 INTER HY
F92/W305 A F92 CE1 B W305 CE3 4.27 INTER HY
F92/W305 A F92 CE1 B W305 CZ3 3.98 INTER HY
F92/V312 A F92 CE2 B V312 CB 4.39 INTER HY
F92/V312 A F92 CE2 B V312 CG2 3.96 INTER HY
F92/V312 A F92 CZ B V312 CG2 4.47 INTER HY
L105/W305 A L105 CG B W305 CH2 4.4 INTER HY
L105/W305 A L105 CD1 B W305 CE3 4.42 INTER HY
L105/W305 A L105 CD1 B W305 CZ2 4.22 INTER HY
L105/W305 A L105 CD1 B W305 CZ3 3.74 INTER HY
L105/W305 A L105 CD1 B W305 CH2 3.63 INTER HY
L105/W305 A L105 CD2 B W305 CZ2 3.87 INTER HY
L105/W305 A L105 CD2 B W305 CH2 3.98 INTER HY
L112/I311 A L112 CD2 B I311 CB 4.3 INTER HY
L112/I311 A L112 CD2 B I311 CG2 3.64 INTER HY
L112/V312 A L112 CD2 B V312 CG2 4.45 INTER HY
E114/R304 A E114 OE2 B R304 NH1 3.37 INTER SB
E114/R304 A E114 OE2 B R304 NH1 3.37 INTER HB
E120/R304 A E120 OE1 B R304 NH2 3.34 INTER SB
E120/R304 A E120 OE1 B R304 NH2 3.34 INTER HB
E120/R304 A E120 OE2 B R304 NH1 3.61 INTER HB
E120/R304 A E120 OE2 B R304 NH2 3.62 INTER HB
E123/R304 A E123 OE2 B R304 NE 5.82 INTER AT
M124/R304 A M124 CG B R304 CB 3.55 INTER HY
M124/R304 A M124 CG B R304 CG 3.85 INTER HY
M124/R304 A M124 CE B R304 CB 3.37 INTER HY
M124/W305 A M124 O B W305 NE1 2.89 INTER HB
M124/W305 A M124 CB B W305 CZ2 4.26 INTER HY
M124/W305 A M124 CE B W305 CB 4.25 INTER HY
M124/W305 A M124 CE B W305 CG 3.55 INTER HY
M124/W305 A M124 CE B W305 CD2 3.47 INTER HY
M124/W305 A M124 CE B W305 CE3 4.05 INTER HY
M124/W305 A M124 CE B W305 CZ2 4.2 INTER HY
E127/R302 A E127 OE1 B R302 N 3.34 INTER HB
E127/R302 A E127 OE1 B R302 NE 5.13 INTER AT
A128/W305 A A128 CB B W305 CZ2 3.98 INTER HY
V136/W305 A V136 CB B W305 CH2 4.44 INTER HY
V136/W305 A V136 CG1 B W305 CH2 4.46 INTER HY
V136/W305 A V136 CG2 B W305 CZ2 4.0 INTER HY
V136/W305 A V136 CG2 B W305 CH2 3.96 INTER HY
F141/W305 A F141 CD2 B W305 CE3 4.46 INTER HY
F141/W305 A F141 CD2 B W305 CZ3 4.08 INTER HY
F141/W305 A F141 CE2 B W305 CE3 4.32 INTER HY
F141/W305 A F141 CE2 B W305 CZ3 4.09 INTER HY
F141/F309 A F141 CE1 B F309 CD1 3.98 INTER HY
F141/F309 A F141 CE1 B F309 CE1 4.19 INTER HY
F141/F309 A F141 CZ B F309 CD1 3.82 INTER HY
F141/F309 A F141 CZ B F309 CE1 4.46 INTER HY
M144/R302 A M144 O B R302 NH1 3.4 INTER HB
M144/R302 A M144 SD B R302 NH1 3.23 INTER HB
M144/W305 A M144 CG B W305 CB 3.87 INTER HY
M144/W305 A M144 CG B W305 CG 3.58 INTER HY
M144/W305 A M144 CG B W305 CD2 3.99 INTER HY
M144/W305 A M144 CE B W305 CG 4.06 INTER HY
M145/W305 A M145 CE B W305 CB 3.91 INTER HY
M145/K306 A M145 CE B K306 CB 4.29 INTER HY
M145/F309 A M145 CG B F309 CB 4.3 INTER HY
M145/F309 A M145 CG B F309 CG 3.7 INTER HY
M145/F309 A M145 CG B F309 CD1 3.68 INTER HY
M145/F309 A M145 CG B F309 CD2 3.92 INTER HY
M145/F309 A M145 CG B F309 CE1 3.88 INTER HY
M145/F309 A M145 CG B F309 CE2 4.13 INTER HY
M145/F309 A M145 CG B F309 CZ 4.1 INTER HY
M145/F309 A M145 CE B F309 CB 3.45 INTER HY
M145/F309 A M145 CE B F309 CG 3.87 INTER HY
M145/F309 A M145 CE B F309 CD2 4.32 INTER HY
K148/K306 A K148 O B K306 NZ 3.41 INTER HB


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