SMTL ID : 7zb3.1

Crystal structure of beta-xylosidase from Thermotoga maritima in complex with xylohexaose hydrolysed to xylobiose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: E.222, F.225, I.252, N.260, K.262, L.263, I.267 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.222, A:F.225, A:I.252, A:K.262 Hydrogen bonds: A:N.260, A:N.260 Water bridges: B:R.223 MPD.3: 7 residues within 4Å: Chain B: E.222, F.225, I.252, N.260, K.262, L.263, I.267 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.222, B:F.225, B:I.252, B:K.262 Hydrogen bonds: B:N.260, B:N.260 Water bridges: A:R.223

2 x IVG: D-Xylose, 4-O-beta-D-xylopyranosyl-(Non-covalent)

IVG.2: 17 residues within 4Å: Chain A: W.35, R.64, E.102, L.150, R.164, K.201, H.202, M.246, Y.249, D.281, Y.282, F.283, Y.415, H.420, L.509, E.517 Chain B: W.620 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.64, A:R.64, A:R.164, A:R.164, A:K.201, A:Y.249, A:D.281, A:Y.415, A:Y.415, A:Y.415, A:H.420, A:E.517 Water bridges: A:E.517 IVG.4: 18 residues within 4Å: Chain A: W.620 Chain B: W.35, R.64, E.102, L.150, R.164, K.201, H.202, W.215, M.246, Y.249, D.281, Y.282, F.283, Y.415, H.420, L.509, E.517 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.64, B:R.64, B:R.164, B:R.164, B:K.201, B:H.202, B:D.281, B:Y.415, B:Y.415, B:Y.415, B:H.420 Water bridges: B:E.167, B:Y.206, B:W.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gloster, T.M. et al., Structural and further functional characterisation of a glycoside hydrolase family 3 beta-xylosidase from Thermotoga maritima. To Be Published

Release Date

2023-04-05

Peptides

Beta-xylosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-xylosidase

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