SMTL ID : 5vl8.1

Coordination Chemistry within a Protein Host: Regulation of the Secondary Coordination Sphere

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x S32: [N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}propyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydroxy)copper(Non-covalent)

S32.1: 23 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, K.121, L.124, D.128 Chain C: W.120, K.121 Ligands: GOL.3, S32.7 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:L.124, C:W.120, C:K.121 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:S.88, A:S.88, A:D.128 Water bridges: A:S.112, A:S.112, A:S.112 S32.4: 23 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, K.121, L.124, D.128 Chain D: W.120, K.121 Ligands: GOL.6, S32.10 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain D, Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, B:L.124, D:W.120, D:K.121 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:S.88, B:S.88, B:D.128 Water bridges: B:S.112, B:S.112, B:S.112 S32.7: 23 residues within 4Å: Chain A: W.120, K.121 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, K.121, L.124, D.128 Ligands: S32.1, GOL.9 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:L.124, A:W.120, A:K.121 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:S.88, C:S.88, C:D.128 Water bridges: C:S.112, C:S.112, C:S.112 S32.10: 23 residues within 4Å: Chain B: W.120, K.121 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, K.121, L.124, D.128 Ligands: S32.4, GOL.12 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, D:L.124, B:W.120, B:K.121 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:S.88, D:S.88, D:D.128 Water bridges: D:S.112, D:S.112, D:S.112

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

CU.2: 1 residues within 4Å: Chain A: H.87 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.87, H2O.3 CU.5: 1 residues within 4Å: Chain B: H.87 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.87, H2O.7 CU.8: 1 residues within 4Å: Chain C: H.87 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.87, H2O.11 CU.11: 1 residues within 4Å: Chain D: H.87 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.87, H2O.14

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: V.47, G.48 Chain C: W.120, K.121 Ligands: S32.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.48, C:W.120, C:K.121 Water bridges: A:A.46, A:G.48 GOL.6: 5 residues within 4Å: Chain B: V.47, G.48 Chain D: W.120, K.121 Ligands: S32.4 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:W.120, D:K.121, B:G.48 Water bridges: B:A.46, B:G.48 GOL.9: 5 residues within 4Å: Chain A: W.120, K.121 Chain C: V.47, G.48 Ligands: S32.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:W.120, A:K.121, C:G.48 Water bridges: C:A.46, C:G.48 GOL.12: 5 residues within 4Å: Chain B: W.120, K.121 Chain D: V.47, G.48 Ligands: S32.10 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:W.120, B:K.121, D:G.48 Water bridges: D:A.46, D:G.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, S.I. et al., Coordination chemistry within a protein host: regulation of the secondary coordination sphere. Chem. Commun. (Camb.) (2018)

Release Date

2018-04-18

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