SMTL ID : 7zdy.1

Crystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 6 residues within 4Å: Chain A: E.222, F.225, I.252, N.260, K.262, I.267 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Water bridges: B:R.223, A:E.222 Hydrophobic interactions: A:E.222, A:F.225, A:I.252, A:K.262 Hydrogen bonds: A:N.260, A:N.260 MPD.2: 4 residues within 4Å: Chain A: D.561, K.562, V.563, N.564 No protein-ligand interaction detected (PLIP) MPD.4: 7 residues within 4Å: Chain A: F.688, A.689, S.690, E.735 Chain B: I.294, R.296, E.300 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.735 MPD.5: 6 residues within 4Å: Chain B: E.222, F.225, I.252, N.260, K.262, I.267 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.222, B:F.225, B:I.252, B:K.262 Hydrogen bonds: B:N.260

2 x 6MJ: methyl beta-D-xylopyranoside(Non-covalent)

6MJ.3: 12 residues within 4Å: Chain A: R.64, E.102, L.150, R.164, K.201, H.202, M.246, Y.249, D.281, Y.282, Y.415, E.517 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.164, A:R.164, A:K.201, A:H.202, A:Y.415, A:E.517 Water bridges: A:R.64, A:Y.206 6MJ.6: 12 residues within 4Å: Chain B: R.64, E.102, L.150, R.164, K.201, H.202, M.246, Y.249, D.281, Y.282, Y.415, E.517 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.164, B:R.164, B:K.201, B:H.202, B:Y.249, B:Y.415, B:E.517 Water bridges: B:R.64, B:E.517

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

2023-04-19

Peptides

Beta-xylosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
W

B
Y

Beta-xylosidase

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