SMTL ID : 2x8f.2 (1 other biounit)

Native structure of Endo-1,5-alpha-L-arabinanases from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 11 residues within 4Å: Chain A: H.37, D.38, S.53, W.100, V.170, D.171, E.224, L.246, Y.252, H.318 Ligands: MRD.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.53, A:S.53, A:E.224, A:Y.252, A:H.318 Water bridges: A:S.188

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: W.93, R.125, M.151, E.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.152, A:E.152 Water bridges: A:G.153, A:G.153 Salt bridges: A:R.125

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: P.172, H.318 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.318, H2O.1, H2O.1, H2O.1, H2O.5

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: D.103, V.104, T.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.104 Water bridges: A:D.103 NA.5: 2 residues within 4Å: Chain A: V.73, Y.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97 Water bridges: A:Y.84

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: T.311, G.312, Y.313, F.338, R.348, R.366, V.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.312, A:R.348 Water bridges: A:S.446 GOL.7: 6 residues within 4Å: Chain A: G.433, K.434, K.435, N.459, T.460, S.461 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.433, A:K.435, A:K.435, A:T.460, A:S.461, A:S.461 GOL.8: 4 residues within 4Å: Chain A: F.353, M.354, L.372, V.439 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.354 Water bridges: A:N.231 GOL.9: 4 residues within 4Å: Chain A: F.48, L.63, D.324, Y.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.324, A:Y.331 GOL.10: 4 residues within 4Å: Chain A: E.43, T.44, N.45, Q.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.43, A:T.44, A:T.44, A:N.45, A:Q.106

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.11: 5 residues within 4Å: Chain A: H.37, H.54, W.100, R.337 Ligands: TRS.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.37 Hydrogen bonds: A:H.37 Water bridges: A:H.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Sanctis, D. et al., New Evidence for the Role of Calcium in the Glycosidase Reaction of Gh43 Arabinanases. FEBS J. (2010)

Release Date

2011-03-23

Peptides

ENDO-ALPHA-1,5-L-ARABINANASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

ENDO-ALPHA-1,5-L-ARABINANASE

Related Entries With Identical Sequence