SMTL ID : 5wbc.1

Designed Artificial Cupredoxins - WT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

4 x CU6: [CuII(biot-et-dpea)]2+(Non-covalent)

CU6.1: 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: GOL.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:N.49, A:A.50, A:W.79, A:W.79, A:W.79, A:L.110, C:W.120 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:N.49, A:A.86, A:S.88, A:S.88, A:D.128 CU6.4: 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: GOL.5 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:N.49, B:A.50, B:W.79, B:W.79, B:W.79, B:L.110, D:W.120 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:N.49, B:A.86, B:S.88, B:S.88, B:D.128 CU6.7: 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: GOL.8 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:N.49, C:A.50, C:W.79, C:W.79, C:W.79, C:L.110, A:W.120 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:N.49, C:A.86, C:S.88, C:S.88, C:D.128 CU6.10: 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: GOL.11 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:N.49, D:A.50, D:W.79, D:W.79, D:W.79, D:L.110, B:W.120 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:N.49, D:A.86, D:S.88, D:S.88, D:D.128

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: V.47, G.48 Chain C: A.117, N.118, W.120, K.121 Ligands: CU6.1, ACT.3 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:A.117, A:G.48 Water bridges: A:A.46, A:G.48 GOL.5: 8 residues within 4Å: Chain B: V.47, G.48 Chain D: A.117, N.118, W.120, K.121 Ligands: CU6.4, ACT.6 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:A.117, B:G.48 Water bridges: B:A.46, B:G.48 GOL.8: 8 residues within 4Å: Chain A: A.117, N.118, W.120, K.121 Chain C: V.47, G.48 Ligands: CU6.7, ACT.9 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.48, A:A.117 Water bridges: C:A.46, C:G.48 GOL.11: 8 residues within 4Å: Chain B: A.117, N.118, W.120, K.121 Chain D: V.47, G.48 Ligands: CU6.10, ACT.12 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:A.117, D:G.48 Water bridges: D:A.46, D:G.48

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

ACT.3: 2 residues within 4Å: Chain A: R.84 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.84 ACT.6: 2 residues within 4Å: Chain B: R.84 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.84 ACT.9: 2 residues within 4Å: Chain C: R.84 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.84 ACT.12: 2 residues within 4Å: Chain D: R.84 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, S.I. et al., Modular Artificial Cupredoxins. J. Am. Chem. Soc. (2016)

Release Date

2017-08-16

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin

Related Entries With Identical Sequence