SMTL ID : 3ada.1

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with sulfite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: V.133, G.134, A.135, G.136, P.137, A.138, D.157, E.158, R.159, G.164, T.165, T.202, T.203, V.204, A.247, T.248, A.249, S.294, F.380, L.386, G.416, A.417, L.422, D.423, T.424, A.427, Y.553 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.380, A:F.380, A:L.422 Hydrogen bonds: A:G.136, 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:A.417, A:D.423, A:T.424 Water bridges: A:A.135, A:G.136, A:G.139, A:G.164, A:A.249, A:A.250, A:N.292, A:L.418, A:L.422, A:T.424

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

SO4.2: 4 residues within 4Å: Chain A: R.597, L.631, T.692, T.693 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.693, A:T.693 Water bridges: A:R.597, A:R.597 Salt bridges: A:R.597 SO4.3: 4 residues within 4Å: Chain A: N.651, G.652, S.847, L.849 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.652, A:S.847 SO4.4: 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 SO4.5: 7 residues within 4Å: Chain A: R.574, T.693, A.696, A.697, S.720, T.722 Chain C: R.171 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.696, A:A.697, A:S.720, A:T.722 Water bridges: A:R.574, A:K.633, A:K.633 Salt bridges: A:R.574, C:R.171 SO4.6: 3 residues within 4Å: Chain A: S.7, A.8, R.18 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.8 Water bridges: A:S.7, A:A.9, A:R.18, A:R.18 Salt bridges: A:R.18 SO4.7: 3 residues within 4Å: Chain A: Q.217, R.219 Chain C: V.194 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.217 Salt bridges: A:R.219 Water bridges: C:V.194 SO4.11: 4 residues within 4Å: Chain C: A.20, G.21, E.22, R.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.22, C:R.23 Salt bridges: C:R.23 SO4.13: 1 residues within 4Å: Chain D: R.83 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.83

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

FAD.8: 36 residues within 4Å: Chain B: V.21, G.22, G.23, G.24, G.25, H.26, L.46, E.47, K.48, G.54, N.55, M.56, R.58, N.59, T.60, T.61, I.62, C.189, E.190, V.191, A.219, G.220, A.221, H.223, L.227, L.242, A.244, G.321, V.323, W.347, G.348, T.349, G.350, G.351, F.352, K.353 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:L.242, B:L.242, B:A.244 Hydrogen bonds: B:G.25, B:H.26, B:K.48, B:G.54, B:N.55, B:N.55, B:M.56, B:N.59, B:T.60, B:I.62, B:I.62, B:V.191, B:V.191, B:G.348, B:G.351, B:F.352, B:K.353, B:K.353 Water bridges: B:G.23, B:G.24, B:G.24, B:E.47, B:K.48, B:K.48, B:G.49, B:W.50, B:G.53, B:N.55, B:N.344 Salt bridges: B:H.26 pi-Cation interactions: B:K.48

1 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.9: 18 residues within 4Å: Chain A: K.509, R.510, T.516, Q.520, T.548, R.550 Chain B: A.57, R.58, N.59, T.61, K.166, H.167, V.246, K.272, E.274, R.317, W.319 Ligands: SO3.10 23 PLIP interactions: 12 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:T.61, B:V.246, B:W.319, B:W.319 Hydrogen bonds: B:K.272, B:R.317, B:R.317, A:K.509, A:R.510, A:T.516, A:Q.520, A:T.548 Water bridges: B:R.58, B:R.58, A:K.509, A:T.548, A:R.550 Salt bridges: B:R.58, B:R.317, A:K.509, A:R.510, A:R.550 pi-Cation interactions: B:K.166

1 x SO3: SULFITE ION(Non-covalent)

SO3.10: 6 residues within 4Å: Chain A: T.516 Chain B: K.166, D.168, K.272, E.274 Ligands: FMN.9 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.516, B:K.166, B:K.166, B:K.272 Salt bridges: B:E.274

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 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

Moriguchi, T. et al., Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. J.Biochem. (2010)

Release Date

2010-08-25

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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