SMTL ID : 1x31.2 (2 other biounits)

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Q.30 Chain G: A.25, G.26, E.27, R.28 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: R.574, T.693, A.696, A.697, T.722 Chain C: R.176 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.597, L.631, T.692, T.693 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: N.651, G.652, S.847, L.849 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: E.445, K.446, I.447 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain B: P.8, E.9, F.10, R.181 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: Q.217, R.219 Chain C: V.199 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain D: R.83 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain C: A.25, G.26, E.27, R.28 Chain E: Q.30 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain E: R.574, T.693, A.696, A.697, T.722 Chain G: R.176 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain E: R.597, L.631, T.692, T.693 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain E: N.651, G.652, S.847, L.849 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain E: E.445, K.446, I.447 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain F: P.8, E.9, F.10, R.181 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: Q.217, R.219 Chain G: V.199 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain H: R.83 Ligand excluded by PLIP

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

NAD.6: 27 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, 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:A.417, A:D.423, A:T.424 Water bridges: A:A.135, A:G.136, A:G.136, A:G.164, A:A.249, A:A.250, A:A.250, A:N.292, A:L.418, A:L.422, A:T.424 NAD.19: 27 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, 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:A.417, E:D.423 Water bridges: E:A.135, E:G.136, E:G.136, E:G.164, E:A.249, E:A.250, E:A.250, E:N.292, E:L.418, E:L.422, E:T.424, E:Y.553

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

FAD.8: 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.10 32 PLIP interactions: 32 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: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:K.53, B:G.58, B:N.60, B:G.227 Salt bridges: B:H.31 pi-Cation interactions: B:K.53 FAD.21: 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.23 34 PLIP interactions: 34 interactions with chain F Hydrophobic interactions: F:N.64, F:L.247, F:L.247, F:A.249 Hydrogen bonds: F:G.30, F:H.31, F:K.53, 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:K.53, F:G.58, F:N.60, F:E.195, F:G.227 Salt bridges: F:H.31 pi-Cation interactions: F:K.53

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 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 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:T.66, 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, A:K.509, A:T.548 Salt bridges: B:R.63, B:R.322, A:K.509, A:R.550 FMN.22: 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 20 PLIP interactions: 11 interactions with chain F, 9 interactions with chain E Hydrophobic interactions: F:T.66, F:W.324, F:W.324 Hydrogen bonds: F:K.277, F:E.279, F:R.322, F:R.322, E:K.509, E:R.510, E:T.516, E:Q.520 Water bridges: F:R.63, F:R.63, E:K.509, E:T.516, E:T.548 Salt bridges: F:R.63, F:R.322, E:K.509, E:R.550

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

DMG.10: 8 residues within 4Å: Chain B: T.65, I.67, R.69, M.264, T.354, K.358, A.401 Ligands: FAD.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.65 Water bridges: B:T.354, B:A.401 Salt bridges: B:R.69, B:K.358 DMG.23: 8 residues within 4Å: Chain F: T.65, I.67, R.69, M.264, T.354, K.358, A.401 Ligands: FAD.21 4 PLIP interactions: 4 interactions with chain F Water bridges: F:T.354, F:A.401 Salt bridges: F:R.69, F:K.358

2 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 ZN.25: 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

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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