SMTL ID : 8c7f.1 (1 other biounit)

Crystal structure of beta-xylosidase mutant (D281N, E517Q) from Thermotoga maritima in complex with xylopentaose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

2 x XYP- XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose

XYP-XYP-XYP.1: 16 residues within 4Å: Chain A: H.619, W.620 Chain B: R.64, E.102, L.150, R.164, K.201, H.202, W.215, M.246, Y.249, N.281, Y.282, F.283, Y.415, Q.517 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.164, B:R.164, B:K.201, B:H.202, B:N.281, B:N.281, B:Y.415, B:Q.517 XYP-XYP-XYP.5: 16 residues within 4Å: Chain C: H.619, W.620 Chain D: R.64, E.102, L.150, R.164, K.201, H.202, W.215, M.246, Y.249, N.281, Y.282, F.283, Y.415, Q.517 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.164, D:R.164, D:K.201, D:Y.249, D:N.281, D:N.281, D:Q.517 Water bridges: D:Y.206

2 x XYP- XYP- XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose

XYP-XYP-XYP-XYP.2: 16 residues within 4Å: Chain A: R.64, E.102, L.150, R.164, K.201, H.202, W.215, M.246, Y.249, N.281, Y.282, F.283, Y.415, Q.517 Chain B: H.619, W.620 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.620 XYP-XYP-XYP-XYP.6: 16 residues within 4Å: Chain C: R.64, E.102, L.150, R.164, K.201, H.202, W.215, M.246, Y.249, N.281, Y.282, F.283, Y.415, Q.517 Chain D: H.619, W.620 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.620

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

MPD.3: 8 residues within 4Å: Chain A: E.222, F.225, I.252, V.255, N.260, K.262, L.263, I.267 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.222, A:F.225, A:I.252 Hydrogen bonds: A:N.260 MPD.4: 8 residues within 4Å: Chain B: E.222, F.225, I.252, V.255, N.260, K.262, L.263, I.267 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.222, B:K.262 Hydrogen bonds: B:N.260 MPD.7: 8 residues within 4Å: Chain C: E.222, F.225, I.252, V.255, N.260, K.262, L.263, I.267 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.222, C:F.225, C:I.252 Hydrogen bonds: C:N.260 MPD.8: 8 residues within 4Å: Chain D: E.222, F.225, I.252, V.255, N.260, K.262, L.263, I.267 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:E.222, D:K.262 Hydrogen bonds: D:N.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2024-01-24

Peptides

Xylosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Xylosidase

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