SMTL ID : 3juu.1 (1 other biounit)

Crystal structure of porphyranase B (PorB) from Zobellia galactanivorans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

MES.1: 10 residues within 4Å: Chain A: W.54, R.57, Y.98, W.126, I.128, R.174, R.239 Ligands: SO4.5, GOL.6, GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.57 Water bridges: A:W.54 Salt bridges: A:R.239 pi-Cation interactions: A:W.54, A:W.54

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

SO4.2: 3 residues within 4Å: Chain A: H.13, W.269, R.271 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.13, A:R.271 SO4.3: 3 residues within 4Å: Chain A: G.39, K.40, K.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.40, A:K.41 Salt bridges: A:K.40 SO4.4: 4 residues within 4Å: Chain A: T.77, T.79, K.260, R.263 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.260, A:R.263 SO4.5: 4 residues within 4Å: Chain A: I.128, R.174, N.175 Ligands: MES.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.175 Water bridges: A:T.141 Salt bridges: A:R.174

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: W.54, R.57, T.124, W.126, E.143, D.145, E.148, V.241, E.243 Ligands: MES.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.57, A:R.57, A:T.124, A:E.148 GOL.7: 4 residues within 4Å: Chain A: W.54, G.56, R.57 Ligands: MES.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.56, A:R.57 Water bridges: A:A.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hehemann, J.H. et al., Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature (2010)

Release Date

2010-04-07

Peptides

porphyranase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

porphyranase B

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