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

Protein crystal structure of xylanase A1 of Paenibacillus sp. JDR-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x XYS- XYP- XYP- GCV: 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose(Non-functional Binders)

XYS-XYP-XYP-GCV.1: 14 residues within 4Å: Chain A: G.44, N.45, K.48, H.81, W.85, Q.88, N.137, E.138, Q.232, H.234, E.262, W.305, W.313 Ligands: GOL.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.45, A:K.48, A:H.81, A:N.137, A:N.137, A:Q.232, A:E.262 Salt bridges: A:H.234

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: A.20, G.44, W.305, G.306, T.311, S.312, W.313 Ligands: XYS-XYP-XYP-GCV.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.45, A:T.311, A:S.312, A:W.313 GOL.3: 4 residues within 4Å: Chain A: S.22, A.23, N.45 Ligands: MG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.23, A:N.45 GOL.5: 2 residues within 4Å: Chain A: S.184, W.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.184, A:S.184 Water bridges: A:N.182 GOL.8: 2 residues within 4Å: Chain A: Q.87, Q.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.87, A:Q.88 Water bridges: A:S.89 GOL.9: 4 residues within 4Å: Chain A: G.107, R.108, D.109, E.110 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.107, A:D.109, A:E.110 Water bridges: A:G.107, A:R.108

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: N.182, P.183, S.184 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: K.70 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: G.28, T.29 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 8 residues within 4Å: Chain A: I.21, S.22, A.43, G.44, N.45, A.46, M.67 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St John, F.J. et al., Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2. J.Struct.Biol. (2012)

Release Date

2012-04-04

Peptides

Endo-1,4-beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase

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