SMTL ID : 3ad7.1

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

Coordinates

PDB Format

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: 26 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, Y.553 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:F.380, A:F.380, A:L.422 Hydrogen bonds: A:A.135, 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:E.172, A:A.250, A:A.250, A:N.292, A:L.418, A:L.418, A:L.422, A:T.424

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

SO4.2: 4 residues within 4Å: Chain A: R.597, L.631, T.692, T.693 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.693, A:T.693, A:T.693 Water bridges: A:R.597, 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.652, A:S.847 Water bridges: A:G.652, A:R.662, A:K.848 SO4.4: 3 residues within 4Å: Chain A: S.7, A.8, R.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.8 Water bridges: A:R.18, A:R.18 SO4.5: 2 residues within 4Å: Chain A: Q.217, R.219 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:V.194 Hydrogen bonds: A:Q.217 Salt bridges: A:R.219 SO4.6: 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 SO4.10: 5 residues within 4Å: Chain A: S.513 Chain B: H.7, K.171, H.174, K.277 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.171, B:H.174, B:H.174 Salt bridges: B:H.7, B:K.171 SO4.11: 2 residues within 4Å: Chain B: N.13, N.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.14, B:N.14 SO4.12: 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 SO4.14: 2 residues within 4Å: Chain D: P.7, R.83 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.7 Salt bridges: D:R.83

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

FAD.7: 37 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, A.249, G.326, V.328, W.352, G.353, T.354, G.355, G.356, F.357, K.358 Ligands: MTG.9 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:N.64, 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: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, B:G.227, B:H.228, B:N.349 Salt bridges: B:H.31 pi-Cation interactions: B:K.53

1 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.8: 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 23 PLIP interactions: 12 interactions with chain B, 11 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, A:K.509, A:R.510, A:T.516, A:Q.520, A:T.548 Water bridges: B:R.63, B:R.63, B:R.63, A:K.509, A:T.548, A:T.548 Salt bridges: B:R.63, B:R.322, A:K.509, A:R.510, A:R.550

1 x MTG: [METHYLTHIO]ACETATE(Non-covalent)

MTG.9: 11 residues within 4Å: Chain B: T.65, I.67, R.69, Y.72, M.264, Y.271, T.354, K.358, A.400, V.402 Ligands: FAD.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.400 Salt bridges: B:R.69, B:K.358

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 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

Subunit alpha of sarcosine oxidase: A
Subunit beta of sarcosine oxidase: B
Subunit gamma of sarcosine oxidase: C
Subunit delta of sarcosine oxidase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Subunit alpha of sarcosine oxidase

Subunit beta of sarcosine oxidase

Subunit gamma of sarcosine oxidase

Subunit delta of sarcosine oxidase

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