SMTL ID : 3ad8.1

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate

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: 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 28 PLIP interactions: 28 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.164, A:A.247, A:A.250, A:A.250, A:N.292, A:L.418, A:L.418, A:L.422, A:T.424

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

SO4.2: 4 residues within 4Å: Chain A: R.597, L.631, T.692, T.693 8 PLIP interactions: 8 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, A:G.694 Salt bridges: A:R.597 SO4.3: 4 residues within 4Å: Chain A: N.651, G.652, S.847, L.849 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.652, A:S.847 Water bridges: A:G.652, A:R.662, A:K.848, A:K.848 SO4.4: 2 residues within 4Å: Chain A: S.7, A.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.8, A:R.18 SO4.5: 3 residues within 4Å: Chain A: Q.217, R.219 Chain C: V.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217 Salt bridges: A:R.219 SO4.6: 2 residues within 4Å: Chain A: R.686 Chain C: Q.97 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.686 Hydrogen bonds: C:Q.97 SO4.7: 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 SO4.8: 7 residues within 4Å: Chain A: R.574, T.693, A.696, A.697, S.720, T.722 Chain C: R.171 8 PLIP interactions: 7 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:K.633, A:K.633 Salt bridges: A:R.574, C:R.171 SO4.12: 2 residues within 4Å: Chain B: N.13, N.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.14 SO4.13: 4 residues within 4Å: Chain B: P.8, E.9, F.10, R.181 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.9, B:F.10, B:R.181 SO4.14: 6 residues within 4Å: Chain A: R.487, S.513 Chain B: H.7, K.171, H.174, K.277 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.487 Water bridges: B:K.171 Salt bridges: B:H.7, B:K.171, B:K.277 SO4.15: 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 SO4.17: 2 residues within 4Å: Chain D: P.7, R.83 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.83

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

FAD.9: 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: PYC.11 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:L.247, B:L.247, B:A.249, B:V.328 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 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:N.349 Salt bridges: B:H.31 pi-Cation interactions: B:K.53

1 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.10: 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 22 PLIP interactions: 10 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:K.509, A:R.510, A:T.516, A:Q.520, A:T.548, B:A.62, B:K.277, B:R.322, B:R.322 Water bridges: A:K.509, A:T.548, B:R.63, B:R.63 Salt bridges: A:K.509, A:R.510, 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 PYC: PYRROLE-2-CARBOXYLATE(Non-covalent)

PYC.11: 11 residues within 4Å: Chain B: T.65, I.67, R.69, Y.72, M.264, Y.271, T.354, G.355, K.358, V.402 Ligands: FAD.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.67, B:V.402 Hydrogen bonds: B:T.354, B:T.354 Water bridges: B:Y.72, B:Y.72 Salt bridges: B:R.69, B:K.358 pi-Stacking: B:Y.271

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 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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