SMTL ID : 2q9u.1

Crystal structure of the flavodiiron protein from Giardia intestinalis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

10 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 11 residues within 4Å: Chain A: F.30, H.31, E.87, D.89, H.152, D.171, H.176, Y.199, I.203, H.230 Ligands: FEO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.199 NO3.2: 6 residues within 4Å: Chain A: D.264, M.323, P.324, S.325 Chain C: G.32, I.298 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.264, A:S.325, A:S.325, C:G.32 Water bridges: A:S.325 NO3.3: 5 residues within 4Å: Chain A: R.282 Chain B: Q.11, E.12, M.13, R.182 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.282, A:R.282 Water bridges: B:Q.9, B:E.186, B:E.186 NO3.6: 10 residues within 4Å: Chain B: H.31, E.87, D.89, H.152, D.171, H.176, Y.199, I.203, H.230 Ligands: FEO.9 No protein-ligand interaction detected (PLIP) NO3.7: 6 residues within 4Å: Chain B: G.32, I.298 Chain D: D.264, M.323, P.324, S.325 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:G.32, D:S.325, D:S.325 Water bridges: D:S.325 NO3.10: 11 residues within 4Å: Chain C: F.30, H.31, E.87, D.89, H.152, D.171, H.176, Y.199, I.203, H.230 Ligands: FEO.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.199 NO3.11: 6 residues within 4Å: Chain A: G.32, I.298 Chain C: D.264, M.323, P.324, S.325 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.264, C:S.325, C:S.325, A:G.32 Water bridges: C:S.325 NO3.12: 5 residues within 4Å: Chain C: R.282 Chain D: Q.11, E.12, M.13, R.182 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Water bridges: D:Q.9, D:E.186, D:E.186 Hydrogen bonds: C:R.282, C:R.282 NO3.15: 10 residues within 4Å: Chain D: H.31, E.87, D.89, H.152, D.171, H.176, Y.199, I.203, H.230 Ligands: FEO.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.230 NO3.16: 6 residues within 4Å: Chain B: D.264, M.323, P.324, S.325 Chain D: G.32, I.298 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.32, B:S.325, B:S.325 Water bridges: B:S.325

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 20 residues within 4Å: Chain A: S.265, M.266, Y.267, G.268, T.269, T.270, P.316, T.317, L.318, N.319, N.320, A.349, F.350, G.351, W.352, S.353, F.382 Chain C: H.31, E.87, W.153 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.267, A:L.318, C:W.153 Hydrogen bonds: A:M.266, A:Y.267, A:G.268, A:T.269, A:T.269, A:T.270, A:T.270, A:T.317, A:T.317, A:N.319, A:N.320, A:G.351, A:W.352, A:S.353, A:S.353, A:F.382 Water bridges: A:N.320 pi-Stacking: A:W.352, A:W.352 FMN.8: 20 residues within 4Å: Chain B: S.265, M.266, Y.267, G.268, T.269, T.270, P.316, T.317, L.318, N.319, N.320, A.349, F.350, G.351, W.352, S.353, F.382 Chain D: H.31, E.87, W.153 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.267, B:L.318, D:W.153 Hydrogen bonds: B:M.266, B:Y.267, B:G.268, B:T.269, B:T.269, B:T.269, B:T.270, B:T.317, B:T.317, B:N.319, B:N.320, B:G.351, B:W.352, B:S.353, B:S.353, B:F.382 Water bridges: B:N.320 pi-Stacking: B:W.352 FMN.13: 20 residues within 4Å: Chain A: H.31, E.87, W.153 Chain C: S.265, M.266, Y.267, G.268, T.269, T.270, P.316, T.317, L.318, N.319, N.320, A.349, F.350, G.351, W.352, S.353, F.382 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.267, C:L.318, A:W.153 Hydrogen bonds: C:M.266, C:Y.267, C:G.268, C:T.269, C:T.269, C:T.270, C:T.270, C:T.317, C:T.317, C:N.319, C:N.320, C:G.351, C:W.352, C:S.353, C:S.353, C:F.382 Water bridges: C:N.320 pi-Stacking: C:W.352, C:W.352 FMN.17: 20 residues within 4Å: Chain B: H.31, E.87, W.153 Chain D: S.265, M.266, Y.267, G.268, T.269, T.270, P.316, T.317, L.318, N.319, N.320, A.349, F.350, G.351, W.352, S.353, F.382 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.267, D:L.318, B:W.153 Hydrogen bonds: D:M.266, D:Y.267, D:G.268, D:T.269, D:T.269, D:T.269, D:T.270, D:T.317, D:T.317, D:N.319, D:N.320, D:G.351, D:W.352, D:S.353, D:S.353, D:F.382 Water bridges: D:N.320 pi-Stacking: D:W.352

4 x FEO: MU-OXO-DIIRON(Non-covalent)

FEO.5: 8 residues within 4Å: Chain A: H.85, E.87, D.89, H.90, H.152, D.171, H.230 Ligands: NO3.1 8 PLIP interactions: 8 interactions with chain A, Metal complexes: A:H.85, A:E.87, A:D.89, A:H.90, A:H.152, A:D.171, A:D.171, A:H.230 FEO.9: 8 residues within 4Å: Chain B: H.85, E.87, D.89, H.90, H.152, D.171, H.230 Ligands: NO3.6 8 PLIP interactions: 8 interactions with chain B, Metal complexes: B:H.85, B:E.87, B:D.89, B:H.90, B:H.152, B:D.171, B:D.171, B:H.230 FEO.14: 8 residues within 4Å: Chain C: H.85, E.87, D.89, H.90, H.152, D.171, H.230 Ligands: NO3.10 8 PLIP interactions: 8 interactions with chain C, Metal complexes: C:H.85, C:E.87, C:D.89, C:H.90, C:H.152, C:D.171, C:D.171, C:H.230 FEO.18: 8 residues within 4Å: Chain D: H.85, E.87, D.89, H.90, H.152, D.171, H.230 Ligands: NO3.15 8 PLIP interactions: 8 interactions with chain D, Metal complexes: D:H.85, D:E.87, D:D.89, D:H.90, D:H.152, D:D.171, D:D.171, D:H.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Matteo, A. et al., The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J.Biol.Chem. (2008)

Release Date

2007-12-11

Peptides

A-type flavoprotein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

A-type flavoprotein