SMTL ID : 6ui0.1

Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

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

QFY.1: 26 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, E.112, A.121, S.122, T.123, L.124, D.128 Chain C: W.120, A.121, L.124 Ligands: ACT.2, ACT.3 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:L.110, A:E.112, A:L.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 Salt bridges: A:E.112 Metal complexes: A:E.112 QFY.7: 26 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, E.112, A.121, S.122, T.123, L.124, D.128 Chain D: W.120, A.121, L.124 Ligands: ACT.8, ACT.9 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, B:L.110, B:E.112, B:L.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 Salt bridges: B:E.112 Metal complexes: B:E.112 QFY.13: 26 residues within 4Å: Chain A: W.120, A.121, L.124 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, E.112, A.121, S.122, T.123, L.124, D.128 Ligands: ACT.14, ACT.15 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:L.110, C:E.112, C:L.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 Salt bridges: C:E.112 Metal complexes: C:E.112 QFY.19: 26 residues within 4Å: Chain B: W.120, A.121, L.124 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, E.112, A.121, S.122, T.123, L.124, D.128 Ligands: ACT.20, ACT.21 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, D:L.110, D:E.112, D:L.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 Salt bridges: D:E.112 Metal complexes: D:E.112

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

ACT.2: 3 residues within 4Å: Chain A: E.112 Ligands: QFY.1, ACT.3 Ligand excluded by PLIP ACT.3: 5 residues within 4Å: Chain A: N.49, A.86, E.112 Ligands: QFY.1, ACT.2 Ligand excluded by PLIP ACT.4: 1 residues within 4Å: Chain A: Y.83 Ligand excluded by PLIP ACT.5: 1 residues within 4Å: Chain A: R.84 Ligand excluded by PLIP ACT.6: 1 residues within 4Å: Chain A: H.87 Ligand excluded by PLIP ACT.8: 3 residues within 4Å: Chain B: E.112 Ligands: QFY.7, ACT.9 Ligand excluded by PLIP ACT.9: 5 residues within 4Å: Chain B: N.49, A.86, E.112 Ligands: QFY.7, ACT.8 Ligand excluded by PLIP ACT.10: 1 residues within 4Å: Chain B: Y.83 Ligand excluded by PLIP ACT.11: 1 residues within 4Å: Chain B: R.84 Ligand excluded by PLIP ACT.12: 1 residues within 4Å: Chain B: H.87 Ligand excluded by PLIP ACT.14: 3 residues within 4Å: Chain C: E.112 Ligands: QFY.13, ACT.15 Ligand excluded by PLIP ACT.15: 5 residues within 4Å: Chain C: N.49, A.86, E.112 Ligands: QFY.13, ACT.14 Ligand excluded by PLIP ACT.16: 1 residues within 4Å: Chain C: Y.83 Ligand excluded by PLIP ACT.17: 1 residues within 4Å: Chain C: R.84 Ligand excluded by PLIP ACT.18: 1 residues within 4Å: Chain C: H.87 Ligand excluded by PLIP ACT.20: 3 residues within 4Å: Chain D: E.112 Ligands: QFY.19, ACT.21 Ligand excluded by PLIP ACT.21: 5 residues within 4Å: Chain D: N.49, A.86, E.112 Ligands: QFY.19, ACT.20 Ligand excluded by PLIP ACT.22: 1 residues within 4Å: Chain D: Y.83 Ligand excluded by PLIP ACT.23: 1 residues within 4Å: Chain D: R.84 Ligand excluded by PLIP ACT.24: 1 residues within 4Å: Chain D: H.87 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, K.R. et al., Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases. Inorg.Chem. (2020)

Release Date

2020-05-06

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin

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