SMTL ID : 4h41.1

Crystal structure of a putative alpha-L-fucosidase (BT_0435) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x UNL: UNKNOWN LIGAND

UNL.1: 16 residues within 4Å: Chain A: F.38, H.44, D.45, I.46, I.74, R.75, Y.161, E.165, S.196, Q.243, N.273, E.275, F.277, R.279, F.285, F.311 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:D.45, A:E.165, A:S.196, A:Q.243, A:N.273, A:R.279 Water bridges: A:H.44, A:R.75, A:R.75, A:Y.161, A:E.165, A:Q.243, A:Q.243, A:E.275, A:R.279, A:R.279 UNL.10: 17 residues within 4Å: Chain B: F.38, H.44, D.45, I.46, I.74, R.75, Y.161, E.165, S.196, Q.243, N.273, E.275, F.277, R.279, F.285, F.311 Ligands: 1PE.11 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.165, B:S.196, B:Q.243, B:N.273, B:R.279 Water bridges: B:H.44, B:R.75, B:R.75, B:Y.161, B:E.165, B:Q.243, B:E.275, B:R.279 UNL.17: 16 residues within 4Å: Chain C: F.38, H.44, D.45, I.46, I.74, R.75, Y.161, E.165, S.196, Q.243, N.273, E.275, F.277, R.279, F.285, F.311 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:D.45, C:D.45, C:E.165, C:E.165, C:N.273, C:E.275, C:R.279 Water bridges: C:S.43, C:R.75, C:Y.161, C:E.165, C:Q.243, C:R.279

7 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 6 residues within 4Å: Chain A: Y.126, W.127, D.128, T.129, G.130, W.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.130 Water bridges: A:S.167 1PE.3: 4 residues within 4Å: Chain A: H.234, K.265, Y.266, G.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.266 Water bridges: A:H.234 1PE.6: 6 residues within 4Å: Chain A: H.44, D.45, Y.78, R.79, W.127 Chain C: D.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.78 Water bridges: A:R.79 1PE.11: 11 residues within 4Å: Chain A: L.211, D.280 Chain B: H.44, D.45, R.75, Y.78, R.79, W.127, E.165 Ligands: UNL.10, 1PE.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.44, B:Y.78 Water bridges: B:R.79, B:R.79 1PE.15: 7 residues within 4Å: Chain B: Y.126, W.127, D.128, T.129, G.130, W.198 Ligands: 1PE.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.128 1PE.18: 7 residues within 4Å: Chain B: D.280 Chain C: H.44, D.45, Y.78, R.79, W.127 Ligands: 1PE.19 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.78 Water bridges: C:R.79, B:D.280, B:D.280 1PE.19: 9 residues within 4Å: Chain C: Y.126, W.127, D.128, T.129, G.130, S.167, W.198, M.206 Ligands: 1PE.18 No protein-ligand interaction detected (PLIP)

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.4: 8 residues within 4Å: Chain A: I.136, E.137, K.140, Y.141, D.144, A.179, Q.183 Ligands: PE4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.140 PE4.5: 9 residues within 4Å: Chain A: D.131, S.133, W.134, I.136, E.137, K.171, G.172, D.175 Ligands: PE4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.131

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 5 residues within 4Å: Chain A: Y.88, K.91, K.92, E.137, Y.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.92 PG4.8: 7 residues within 4Å: Chain A: R.178, A.179, K.182, G.232, E.235, V.236 Ligands: PG4.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.178, A:R.178, A:R.178 Water bridges: A:E.235 PG4.9: 6 residues within 4Å: Chain A: K.182, K.185, D.186, E.235, V.236 Ligands: PG4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.182 PG4.16: 5 residues within 4Å: Chain B: K.260, Q.269, G.304, Y.305, D.306 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.269 PG4.20: 11 residues within 4Å: Chain C: D.69, T.70, N.113, M.114, K.115, K.155, S.156, F.157, G.158, L.191, K.307 No protein-ligand interaction detected (PLIP)

2 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.12: 9 residues within 4Å: Chain B: D.69, N.113, M.114, K.115, K.155, S.156, F.157, G.158, L.191 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.115 PG6.13: 8 residues within 4Å: Chain B: D.131, S.133, W.134, I.136, K.171, G.172, D.175 Ligands: NA.14 No protein-ligand interaction detected (PLIP)

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

NA.14: 2 residues within 4Å: Chain B: S.133 Ligands: PG6.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative alpha-L-fucosidase (BT_0435) from Bacteroides thetaiotaomicron VPI-5482 at 1.80 A resolution. To be published

Release Date

2012-10-10

Peptides

putative alpha-L-fucosidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

putative alpha-L-fucosidase