SMTL ID : 5wba.1

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - WT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x SI8: [N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydrogen peroxido-kappaO)copper(Non-covalent)

SI8.1: 20 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, D.128 Chain C: W.120 Ligands: ACT.2 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:N.49, A:A.50, A:W.79, A:W.79, A:W.79, A:L.110 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:N.49, A:S.88, A:S.88, A:D.128 SI8.5: 20 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, D.128 Chain D: W.120 Ligands: ACT.6 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:N.49, B:A.50, B:W.79, B:W.79, B:W.79, B:L.110 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:N.49, B:S.88, B:S.88, B:D.128 SI8.9: 20 residues within 4Å: Chain A: W.120 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, D.128 Ligands: ACT.10 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:N.49, C:A.50, C:W.79, C:W.79, C:W.79, C:L.110 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:N.49, C:S.88, C:S.88, C:D.128 SI8.13: 20 residues within 4Å: Chain B: W.120 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, D.128 Ligands: ACT.14 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:N.49, D:A.50, D:W.79, D:W.79, D:W.79, D:L.110 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:N.49, D:S.88, D:S.88, D:D.128

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: G.48 Chain C: W.120, K.121 Ligands: SI8.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.48 Salt bridges: C:K.121 ACT.6: 4 residues within 4Å: Chain B: G.48 Chain D: W.120, K.121 Ligands: SI8.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.48 Salt bridges: D:K.121 ACT.10: 4 residues within 4Å: Chain A: W.120, K.121 Chain C: G.48 Ligands: SI8.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:K.121 Hydrogen bonds: C:G.48 ACT.14: 4 residues within 4Å: Chain B: W.120, K.121 Chain D: G.48 Ligands: SI8.13 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.48 Salt bridges: B:K.121

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: G.48, R.84 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.84 Salt bridges: A:R.84 SO4.7: 2 residues within 4Å: Chain B: G.48, R.84 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.84 Salt bridges: B:R.84 SO4.11: 2 residues within 4Å: Chain C: G.48, R.84 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.84 Salt bridges: C:R.84 SO4.15: 2 residues within 4Å: Chain D: G.48, R.84 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.84 Salt bridges: D:R.84

4 x CU: COPPER (II) ION(Non-covalent)

CU.4: 1 residues within 4Å: Chain A: H.87 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.87 CU.8: 1 residues within 4Å: Chain B: H.87 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.87 CU.12: 1 residues within 4Å: Chain C: H.87 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.87 CU.16: 1 residues within 4Å: Chain D: H.87 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, S.I. et al., Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins. J. Am. Chem. Soc. (2017)

Release Date

2017-11-22

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin

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