SMTL ID : 5g5g.1

Escherichia coli Periplasmic Aldehyde Oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 8 residues within 4Å: Chain A: Q.157, C.158, G.159, C.161, C.208, R.209, C.210 Chain C: M.190 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.158, A:C.161, A:C.208, A:C.210 FES.2: 11 residues within 4Å: Chain A: K.97, G.98, C.99, D.100, G.102, Q.103, C.104, G.105, C.107, N.117, C.119 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.99, A:C.104, A:C.107, A:C.119

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 4 residues within 4Å: Chain A: K.97, C.99 Chain C: P.192, R.272 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: H.144 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: Q.249, G.254, R.255 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain B: H.263 Ligands: GOL.18 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain C: A.45, P.46, N.47, P.265 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain C: R.606, K.669 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain C: A.7, N.10, P.684 Ligand excluded by PLIP

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: L.110, G.113, A.171 Ligand excluded by PLIP CL.5: 8 residues within 4Å: Chain A: C.99, H.101, Q.103 Chain C: R.272, P.273, D.655, M.656 Ligands: GOL.8 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: A.54, T.55, P.56 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: P.120, F.144 Chain C: N.653 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: N.130, G.135, K.199 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: R.170, E.269 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: A.308 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain C: Q.14, R.527, Q.542, F.543 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain C: P.21, H.22 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: K.620 Ligands: GOL.9 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain C: I.673, F.674 Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

ACT.7: 3 residues within 4Å: Chain A: R.114 Chain B: T.76, D.77 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.175, B:N.105 Salt bridges: A:R.114 ACT.17: 3 residues within 4Å: Chain B: T.62, D.63, A.64 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.63, B:A.64 Water bridges: B:T.62, B:T.62, B:D.63, B:D.63 ACT.31: 2 residues within 4Å: Chain C: R.440, L.443 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.443 Water bridges: C:T.318, C:G.508 Salt bridges: C:R.440 ACT.32: 6 residues within 4Å: Chain C: P.158, V.320, E.324, T.334, G.335, L.336 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.320, C:L.336 Hydrogen bonds: C:E.324, C:L.336

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: H.101, Q.103 Chain B: D.36, Y.123 Chain C: P.273, D.655 Ligands: CL.5 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:D.36, A:H.101, A:Q.103 Water bridges: C:H.654 GOL.9: 6 residues within 4Å: Chain A: H.153, N.215, A.218 Chain C: K.620, R.623 Ligands: CL.29 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.623, A:H.153 GOL.18: 6 residues within 4Å: Chain B: R.170, K.264, W.266, R.267, I.268 Ligands: IOD.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.170, B:K.264 Water bridges: B:K.264, B:R.267, B:R.267 GOL.19: 6 residues within 4Å: Chain B: Q.147, A.238, F.239 Chain C: A.657, G.658, E.660 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.660, B:F.239 GOL.33: 4 residues within 4Å: Chain C: E.641, Y.717, P.718, K.723 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.717, C:K.723, C:K.723 Water bridges: C:T.181, C:E.641 GOL.34: 6 residues within 4Å: Chain C: I.25, D.26, Y.237, Y.473, A.492, V.493 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.493 Water bridges: C:Y.237, C:Y.237, C:H.494

1 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.11: 12 residues within 4Å: Chain B: C.119, Y.121, F.122, C.129, N.130, K.131, C.138, H.148, A.156, C.157, I.158, A.159 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.119, B:C.129, B:C.138, B:C.157

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.12: 33 residues within 4Å: Chain A: H.101, G.102, Q.103 Chain B: K.26, F.27, A.29, G.30, G.31, T.32, N.33, L.34, A.71, L.72, G.98, A.99, L.103, A.107, T.108, A.110, G.111, N.112, L.114, Q.115, P.162, S.163, D.164, E.211, L.212, I.213, K.230, Y.237, A.238, F.239 33 PLIP interactions: 32 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.103, B:Y.237, B:F.239, A:Q.103 Hydrogen bonds: B:K.26, B:F.27, B:F.27, B:A.29, B:G.30, B:G.31, B:T.32, B:T.32, B:N.33, B:L.34, B:N.75, B:A.99, B:T.108, B:N.112, B:Q.115, B:D.164, B:D.164, B:I.213, B:I.213, B:K.230 Water bridges: B:K.26, B:G.98, B:T.108, B:L.114, B:L.114, B:M.165 pi-Stacking: B:F.27, B:F.239 pi-Cation interactions: B:R.118

1 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)

MCN.22: 36 residues within 4Å: Chain A: Q.157, C.210 Chain C: G.240, G.241, F.242, G.243, R.350, M.465, I.468, G.469, T.470, G.471, S.472, I.475, S.506, G.507, G.508, Q.509, W.510, G.511, A.512, A.613, R.615, I.616, L.617, N.618, T.621, A.622, Q.625, A.687, K.688, G.689, V.690, G.691, E.692 Ligands: MOS.23 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.512, C:V.690 Hydrogen bonds: C:G.241, C:F.242, C:G.507, C:G.511, C:A.512, C:R.615, C:L.617, C:N.618, C:T.621, C:Q.625, C:K.688, C:V.690, C:G.691, A:Q.157 Water bridges: C:R.350, C:T.470, C:N.513, A:Q.157

1 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)

MOS.23: 11 residues within 4Å: Chain C: Q.211, G.243, L.246, A.348, M.349, R.350, P.352, G.507, G.508, E.692 Ligands: MCN.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.211, C:G.508

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Correia, M.A. et al., The Escherichia Coli Periplasmic Aldehyde Oxidoreductase is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. Acs Chem.Biol. (2016)

Release Date

2016-09-28

Peptides

PUTATIVE XANTHINE DEHYDROGENASE YAGT IRON-SULFUR-BINDING SUBUNIT: A
PUTATIVE XANTHINE DEHYDROGENASE YAGR MOLYBDENUM-BINDING SU SUBUNIT: B
PUTATIVE XANTHINE DEHYDROGENASE YAGS FAD-BINDING SUBUNIT: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PUTATIVE XANTHINE DEHYDROGENASE YAGT IRON-SULFUR-BINDING SUBUNIT

PUTATIVE XANTHINE DEHYDROGENASE YAGR MOLYBDENUM-BINDING SU SUBUNIT

PUTATIVE XANTHINE DEHYDROGENASE YAGS FAD-BINDING SUBUNIT

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