SMTL ID : 5vkx.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-tetramer

Ligands

4 x S18: [N-(3-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](azido)copper(Non-covalent)

S18.1: 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.3 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:N.49, A:A.50, 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 Water bridges: A:N.85 S18.4: 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.6 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:N.49, B:A.50, 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 S18.7: 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.9 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:N.49, C:A.50, 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 Water bridges: C:N.85 S18.10: 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.12 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:N.49, D:A.50, 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:A.86, D:S.88, D:S.88, D:D.128

4 x CU: COPPER (II) ION(Non-functional Binders)

CU.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CU.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CU.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CU.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.47, G.48 Chain C: A.117, N.118, W.120, K.121 Ligands: S18.1 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:A.117, A:G.48 Water bridges: A:G.48 GOL.6: 7 residues within 4Å: Chain B: V.47, G.48 Chain D: A.117, N.118, W.120, K.121 Ligands: S18.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.48, D:A.117 Water bridges: B:G.48 GOL.9: 7 residues within 4Å: Chain A: A.117, N.118, W.120, K.121 Chain C: V.47, G.48 Ligands: S18.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.117, C:G.48 Water bridges: C:G.48 GOL.12: 7 residues within 4Å: Chain B: A.117, N.118, W.120, K.121 Chain D: V.47, G.48 Ligands: S18.10 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.48, B:A.117 Water bridges: 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

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