SMTL ID : 5b0s.1

Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannotriose complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MAN- BMA- BMA: beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose

MAN-BMA-BMA.1: 16 residues within 4Å: Chain A: N.31, R.46, R.89, M.90, L.103, E.140, D.141, V.158, K.188, R.246, N.271, Y.273, F.309, F.314, D.333 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.31, A:N.31, A:R.46, A:R.89, A:R.89, A:D.141, A:K.188, A:K.188, A:R.89, A:R.89, A:K.188, A:Y.273 Water bridges: A:D.333 Salt bridges: A:R.89 MAN-BMA-BMA.2: 17 residues within 4Å: Chain B: N.31, R.46, R.89, M.90, L.103, E.140, D.141, V.158, K.188, L.215, R.246, N.271, Y.273, F.309, F.314, D.333 Ligands: SO4.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.31, B:N.31, B:R.46, B:R.89, B:R.89, B:D.141, B:D.141, B:K.188, B:K.188, B:R.89, B:R.89, B:K.188, B:R.246, B:Y.273 Water bridges: B:E.140, B:D.333, B:S.208 Salt bridges: B:R.89

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

SO4.3: 9 residues within 4Å: Chain A: K.188, D.189, R.206, R.246, H.265, Y.273, F.314 Ligands: MAN-BMA-BMA.1, MAN-BMA-BMA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.189, A:Y.273 Salt bridges: A:K.188, A:R.206, A:H.265 SO4.4: 5 residues within 4Å: Chain A: I.147, G.148, D.149, T.150, K.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.149, A:T.150 Salt bridges: A:K.171 SO4.5: 3 residues within 4Å: Chain A: A.301, D.302, Y.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.302, A:D.302 SO4.6: 3 residues within 4Å: Chain A: V.17, K.18, R.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.18 Salt bridges: A:K.18, A:R.110 SO4.7: 2 residues within 4Å: Chain A: Q.179, R.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.179 Salt bridges: A:R.226 SO4.9: 4 residues within 4Å: Chain B: V.17, K.18, R.110, L.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.18, B:K.18 Salt bridges: B:K.18, B:R.110 SO4.10: 9 residues within 4Å: Chain B: K.188, D.189, R.206, R.246, H.265, Y.273, F.314 Ligands: MAN-BMA-BMA.2, MAN-BMA-BMA.2 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.188, B:R.206, B:H.265 SO4.11: 3 residues within 4Å: Chain B: E.177, Q.179, R.226 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.179, B:Q.179 Salt bridges: B:R.226 SO4.12: 1 residues within 4Å: Chain B: R.92 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.92

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 4 residues within 4Å: Chain A: I.20, H.21, E.22, Y.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.22 Water bridges: A:Y.129 MES.15: 7 residues within 4Å: Chain B: I.147, G.148, D.149, T.150, H.152, K.171, Y.201 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.149, B:T.150 Salt bridges: B:K.171 MES.16: 4 residues within 4Å: Chain B: I.20, H.21, E.22, Y.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.22

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain B: H.233, L.234, L.235, G.236, R.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.236, B:R.291 GOL.14: 5 residues within 4Å: Chain A: Y.178, Q.179, G.180 Chain B: D.230, R.232 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.232 Water bridges: B:D.230, A:Y.178, A:Q.179, A:N.181, A:N.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsuda, T. et al., Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua. Febs Lett. (2015)

Release Date

2015-12-02

Peptides

Lin0857 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lin0857 protein

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