SMTL ID : 7kby.1

Artificial Metalloproteins with Dinuclear Iron Centers

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x KM3: {N-(4-{bis[(pyridin-2-yl-kappaN)methyl]amino-kappaN}butyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}iron(3+)(Covalent)

KM3.1: 24 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, A.121, Y.124, D.128 Chain C: W.120, A.121 Ligands: CYN.2, KM3.7, CYN.8 17 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions, Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:Y.124, C:A.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 Metal complexes: A:Y.124, H2O.1, H2O.6 KM3.4: 24 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, A.121, Y.124, D.128 Chain D: W.120, A.121 Ligands: CYN.5, KM3.10, CYN.11 16 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions, Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, B:Y.124, D:A.121 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:S.88, B:S.88, B:D.128 Metal complexes: B:Y.124, H2O.3, H2O.9 KM3.7: 24 residues within 4Å: Chain A: W.120, A.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, A.121, Y.124, D.128 Ligands: KM3.1, CYN.2, CYN.8 17 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions, Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:Y.124, A:A.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 Metal complexes: C:Y.124, H2O.1, H2O.6 KM3.10: 24 residues within 4Å: Chain B: W.120, A.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, A.121, Y.124, D.128 Ligands: KM3.4, CYN.5, CYN.11 16 PLIP interactions: 13 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions, Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, D:Y.124, B:A.121 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:S.88, D:S.88, D:D.128 Metal complexes: D:Y.124, H2O.3, H2O.9

4 x CYN: CYANIDE ION(Non-functional Binders)

CYN.2: 3 residues within 4Å: Ligands: KM3.1, KM3.7, CYN.8 No protein-ligand interaction detected (PLIP) CYN.5: 3 residues within 4Å: Ligands: KM3.4, KM3.10, CYN.11 No protein-ligand interaction detected (PLIP) CYN.8: 3 residues within 4Å: Ligands: KM3.1, CYN.2, KM3.7 No protein-ligand interaction detected (PLIP) CYN.11: 3 residues within 4Å: Ligands: KM3.4, CYN.5, KM3.10 No protein-ligand interaction detected (PLIP)

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

ACT.3: 2 residues within 4Å: Chain A: Y.83, R.84 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.84 ACT.6: 2 residues within 4Å: Chain B: Y.83, R.84 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.84 ACT.9: 2 residues within 4Å: Chain C: Y.83, R.84 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.84 ACT.12: 2 residues within 4Å: Chain D: Y.83, R.84 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, K.R. et al., Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers. J.Am.Chem.Soc. (2021)

Release Date

2021-02-03

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin

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