SMTL ID : 1vrq.2 (2 other biounits)

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-oligomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: C.6, C.9, H.59, C.63 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.6, D:C.9, D:H.59, D:C.63 ZN.20: 4 residues within 4Å: Chain H: C.6, C.9, H.59, C.63 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.6, H:C.9, H:H.59, H:C.63

26 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain C: A.25, G.26, E.27, R.28 Chain E: Q.30 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: R.574, A.696, A.697, T.722 Chain C: R.176 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: K.446, I.447 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain B: N.13, N.14, P.15 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: T.709 Chain D: H.24, N.68, A.84, G.85 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: R.487, S.513 Chain B: H.7, K.171, H.174, K.277 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.651, G.652, S.847, L.849 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: H.870, R.929, N.930 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: Q.217, R.219 Chain C: V.199 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: S.1, K.285, L.349, S.350, A.371, D.372 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: Q.489, D.493, Y.511, T.512 Chain B: H.7 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain C: R.119, T.153, P.160 Chain D: S.60, G.62, R.64 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: S.7, A.8, R.18 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain A: Q.30 Chain G: A.25, G.26, E.27, R.28 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain E: R.574, A.696, A.697, T.722 Chain G: R.176 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain E: K.446, I.447 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain F: N.13, N.14, P.15 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain E: T.709 Chain H: H.24, N.68, A.84, G.85 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain E: R.487, S.513 Chain F: H.7, K.171, H.174, K.277 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain E: N.651, G.652, S.847, L.849 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain E: H.870, R.929, N.930 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain E: Q.217, R.219 Chain G: V.199 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain E: S.1, K.285, L.349, S.350, A.371, D.372 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain E: Q.489, D.493, Y.511, T.512 Chain F: H.7 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain G: R.119, T.153, P.160 Chain H: S.60, G.62, R.64 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain E: S.7, A.8, R.18 Ligand excluded by PLIP

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

FAD.15: 38 residues within 4Å: Chain B: V.26, G.27, G.28, G.29, G.30, H.31, L.51, E.52, K.53, G.59, N.60, M.61, R.63, N.64, T.65, T.66, I.67, C.194, E.195, V.196, A.224, G.225, A.226, H.228, L.232, L.247, Q.248, A.249, G.326, V.328, W.352, G.353, T.354, G.355, G.356, F.357, K.358 Ligands: DMG.19 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:L.247, B:L.247, B:L.247, B:A.249 Hydrogen bonds: B:G.30, B:H.31, B:K.53, B:G.59, B:N.60, B:N.60, B:M.61, B:N.64, B:T.65, B:I.67, B:I.67, B:V.196, B:V.196, B:G.353, B:G.356, B:F.357, B:K.358, B:K.358 Water bridges: B:G.28, B:G.29, B:G.32, B:E.52, B:K.53, B:K.53, B:G.58, B:N.60 Salt bridges: B:H.31 pi-Cation interactions: B:K.53 FAD.34: 38 residues within 4Å: Chain F: V.26, G.27, G.28, G.29, G.30, H.31, L.51, E.52, K.53, G.59, N.60, M.61, R.63, N.64, T.65, T.66, I.67, C.194, E.195, V.196, A.224, G.225, A.226, H.228, L.232, L.247, Q.248, A.249, G.326, V.328, W.352, G.353, T.354, G.355, G.356, F.357, K.358 Ligands: DMG.38 34 PLIP interactions: 34 interactions with chain F Hydrophobic interactions: F:L.247, F:L.247, F:L.247, F:A.249 Hydrogen bonds: F:G.30, F:H.31, F:K.53, F:G.59, F:N.60, F:N.60, F:M.61, F:N.64, F:T.65, F:T.65, F:I.67, F:I.67, F:V.196, F:V.196, F:G.353, F:G.356, F:F.357, F:K.358, F:K.358 Water bridges: F:G.28, F:G.29, F:G.32, F:E.52, F:K.53, F:K.53, F:G.58, F:N.60, F:E.195 Salt bridges: F:H.31 pi-Cation interactions: F:K.53

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.16: 28 residues within 4Å: Chain A: V.133, G.134, A.135, G.136, P.137, A.138, L.156, D.157, E.158, R.159, G.164, T.165, T.202, T.203, V.204, A.247, T.248, A.249, N.292, S.294, F.380, L.386, G.416, A.417, L.422, D.423, T.424, Y.553 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.380, A:F.380, A:L.422 Hydrogen bonds: A:A.135, A:A.138, A:E.158, A:E.158, A:R.159, A:R.159, A:T.165, A:T.165, A:T.165, A:V.204, A:V.204, A:N.292, A:A.417, A:D.423, A:T.424 Water bridges: A:G.136, A:G.136, A:D.157, A:G.164, A:A.250, A:A.250, A:L.418, A:L.418, A:L.422, A:T.424 NAD.35: 28 residues within 4Å: Chain E: V.133, G.134, A.135, G.136, P.137, A.138, L.156, D.157, E.158, R.159, G.164, T.165, T.202, T.203, V.204, A.247, T.248, A.249, N.292, S.294, F.380, L.386, G.416, A.417, L.422, D.423, T.424, Y.553 28 PLIP interactions: 28 interactions with chain E Hydrophobic interactions: E:F.380, E:F.380, E:L.422 Hydrogen bonds: E:A.135, E:A.138, E:D.157, E:E.158, E:R.159, E:R.159, E:T.165, E:T.165, E:T.165, E:V.204, E:V.204, E:N.292, E:A.417, E:D.423 Water bridges: E:G.136, E:G.136, E:D.157, E:G.164, E:A.250, E:A.250, E:L.418, E:L.418, E:L.422, E:T.424, E:Y.553

2 x FON: FOLINIC ACID(Non-covalent)

FON.17: 14 residues within 4Å: Chain A: L.631, Y.663, D.676, G.677, V.678, H.690, T.691, I.774, S.775, F.776, E.783, K.822, F.824, W.844 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.663, A:V.678 Hydrogen bonds: A:H.690, A:T.691, A:K.822 Water bridges: A:Y.663 Salt bridges: A:E.783, A:K.822 FON.36: 14 residues within 4Å: Chain E: L.631, Y.663, D.676, G.677, V.678, H.690, T.691, I.774, S.775, F.776, E.783, K.822, F.824, W.844 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.663, E:V.678 Hydrogen bonds: E:H.690, E:T.691, E:K.822 Water bridges: E:Y.663, E:E.783 Salt bridges: E:E.783, E:K.822

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.18: 16 residues within 4Å: Chain A: K.509, R.510, T.516, Q.520, T.548, R.550 Chain B: A.62, R.63, N.64, T.66, H.172, V.251, K.277, E.279, R.322, W.324 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:T.66, B:V.251, B:W.324, B:W.324 Hydrogen bonds: B:K.277, B:R.322, B:R.322, B:R.322, A:K.509, A:R.510, A:T.516, A:Q.520, A:T.548 Water bridges: B:R.63, B:R.63, A:T.548, A:T.548 Salt bridges: B:R.63, B:R.322, A:K.509, A:R.550 FMN.37: 16 residues within 4Å: Chain E: K.509, R.510, T.516, Q.520, T.548, R.550 Chain F: A.62, R.63, N.64, T.66, H.172, V.251, K.277, E.279, R.322, W.324 22 PLIP interactions: 9 interactions with chain E, 13 interactions with chain F Hydrogen bonds: E:K.509, E:R.510, E:T.516, E:Q.520, F:K.277, F:E.279, F:R.322, F:R.322, F:R.322 Water bridges: E:T.516, E:T.548, E:T.548, F:R.63, F:R.63 Salt bridges: E:K.509, E:R.550, F:R.63, F:R.322 Hydrophobic interactions: F:T.66, F:V.251, F:W.324, F:W.324

2 x DMG: N,N-DIMETHYLGLYCINE(Non-covalent)

DMG.19: 10 residues within 4Å: Chain B: T.65, I.67, R.69, Y.72, M.264, T.354, G.355, K.358, A.401 Ligands: FAD.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.65 Water bridges: B:K.358, B:A.401 Salt bridges: B:R.69, B:K.358 DMG.38: 10 residues within 4Å: Chain F: T.65, I.67, R.69, Y.72, M.264, T.354, G.355, K.358, A.401 Ligands: FAD.34 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.72 Water bridges: F:K.358, F:A.401 Salt bridges: F:R.69, F:K.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ida, K. et al., Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. BIOCHEM.BIOPHYS.RES.COMMUN. (2005)

Release Date

2005-07-05

Peptides

Sarcosine oxidase alpha subunit: AE
Sarcosine oxidase beta subunit: BF
Sarcosine oxidase gamma subunit: CG
Sarcosine oxidase delta subunit: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

B
B

F
B

C
C

G
C

D
D

H
D

Sarcosine oxidase alpha subunit

Sarcosine oxidase beta subunit

Sarcosine oxidase gamma subunit

Sarcosine oxidase delta subunit

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