SMTL ID : 6uiy.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-tetramer

Ligands

4 x QG1: {5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-{[(pyridin-2-yl)methyl][(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)pentanamide}iron(2+)(Non-covalent)

QG1.1: 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, E.112, A.121, S.122, T.123, L.124, D.128 Chain C: W.120, A.121 21 PLIP interactions: 16 interactions with chain A, 3 interactions with chain C, 2 Ligand-Water interactions, Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:L.124, A:L.124, C:W.120, C:W.120, 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, H2O.1, H2O.2 QG1.4: 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, E.112, A.121, S.122, T.123, L.124, D.128 Chain D: W.120, A.121 20 PLIP interactions: 3 interactions with chain D, 15 interactions with chain B, 2 Ligand-Water interactions Hydrophobic interactions: D:W.120, D:W.120, D:A.121, B:W.79, B:W.79, B:W.79, B:L.110, B:L.124, B:L.124 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, H2O.6, H2O.7 QG1.7: 23 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, E.112, A.121, S.122, T.123, L.124, D.128 21 PLIP interactions: 16 interactions with chain C, 3 interactions with chain A, 2 Ligand-Water interactions Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:L.124, C:L.124, A:W.120, A:W.120, 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, H2O.10, H2O.11 QG1.10: 23 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, E.112, A.121, S.122, T.123, L.124, D.128 20 PLIP interactions: 15 interactions with chain D, 3 interactions with chain B, 2 Ligand-Water interactions Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, D:L.124, D:L.124, B:W.120, B:W.120, 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, H2O.15, H2O.16

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

ACT.2: 1 residues within 4Å: Chain A: R.84 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.84 ACT.3: 4 residues within 4Å: Chain A: E.14, A.33, G.34, A.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.35 ACT.5: 1 residues within 4Å: Chain B: R.84 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.84 ACT.6: 4 residues within 4Å: Chain B: E.14, A.33, G.34, A.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.35 ACT.8: 1 residues within 4Å: Chain C: R.84 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.84 ACT.9: 4 residues within 4Å: Chain C: E.14, A.33, G.34, A.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.35 ACT.11: 1 residues within 4Å: Chain D: R.84 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.84 ACT.12: 4 residues within 4Å: Chain D: E.14, A.33, G.34, A.35 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.35

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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