SMTL ID : 1vrq.1 (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-1-1-1-1-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.574, A.696, A.697, T.722 Chain C: R.176 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.697, A:S.720 Water bridges: A:R.574, C:R.176 Salt bridges: A:R.574, C:R.176 SO4.2: 2 residues within 4Å: Chain A: K.446, I.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.447, A:I.447 Salt bridges: A:K.446 SO4.3: 4 residues within 4Å: Chain A: N.651, G.652, S.847, L.849 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.652 Water bridges: A:R.662, A:K.848, A:L.849 SO4.4: 3 residues within 4Å: Chain A: H.870, R.929, N.930 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.930 Salt bridges: A:H.870, A:R.929 SO4.5: 3 residues within 4Å: Chain A: Q.217, R.219 Chain C: V.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.217 Water bridges: A:R.219 Salt bridges: A:R.219 SO4.6: 6 residues within 4Å: Chain A: S.1, K.285, L.349, S.350, A.371, D.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1, A:S.1, A:S.350 SO4.7: 5 residues within 4Å: Chain A: Q.489, D.493, Y.511, T.512 Chain B: H.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.7 Hydrogen bonds: A:Q.489 SO4.8: 3 residues within 4Å: Chain A: S.7, A.8, R.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.8 Water bridges: A:R.18, A:R.18 Salt bridges: A:R.18 SO4.11: 3 residues within 4Å: Chain B: N.13, N.14, P.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.14, B:N.14 SO4.12: 6 residues within 4Å: Chain A: R.487, S.513 Chain B: H.7, K.171, H.174, K.277 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.174, A:R.487 Salt bridges: B:H.7, B:K.171, B:K.277 SO4.16: 4 residues within 4Å: Chain C: A.25, G.26, E.27, R.28 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.27, C:E.27, C:R.28 Salt bridges: C:R.28 SO4.18: 5 residues within 4Å: Chain A: T.709 Chain D: H.24, N.68, A.84, G.85 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.24, D:N.68, D:G.85, A:T.709 Water bridges: D:H.24, D:G.85 Salt bridges: D:H.24 SO4.19: 6 residues within 4Å: Chain C: R.119, T.153, P.160 Chain D: S.60, G.62, R.64 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Water bridges: C:R.119, C:R.119, C:R.119, D:R.64, D:R.64 Salt bridges: C:R.119

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

NAD.9: 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

1 x FON: N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid(Non-covalent)

FON.10: 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

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

FAD.13: 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.15 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

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.14: 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 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:K.509, A:R.510, A:T.516, A:Q.520, A:T.548, B:K.277, B:R.322, B:R.322 Water bridges: A:T.548, A:T.548, B:R.63, B:R.63 Salt bridges: A:K.509, A:R.550, B:R.63, B:R.322 Hydrophobic interactions: B:T.66, B:V.251, B:W.324, B:W.324

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

DMG.15: 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.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.65 Water bridges: B:Y.72, B:T.354, B:K.358, B:A.401 Salt bridges: B:R.69, B:K.358

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 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

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: A
Sarcosine oxidase beta subunit: B
Sarcosine oxidase gamma subunit: C
Sarcosine oxidase delta subunit: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Sarcosine oxidase alpha subunit

Sarcosine oxidase beta subunit

Sarcosine oxidase gamma subunit

Sarcosine oxidase delta subunit

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