SMTL ID : 4wva.1 (1 other biounit)

Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with Tris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 8 residues within 4Å: Chain A: H.312, Q.313 Chain B: H.312, Q.313 Chain C: H.312, Q.313 Ligands: CL.6, CL.11 Ligand excluded by PLIP CL.6: 8 residues within 4Å: Chain A: H.312, Q.313 Chain B: H.312, Q.313 Chain C: H.312, Q.313 Ligands: CL.1, CL.11 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain A: H.312, Q.313 Chain B: H.312, Q.313 Chain C: H.312, Q.313 Ligands: CL.1, CL.6 Ligand excluded by PLIP

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 9 residues within 4Å: Chain A: Y.28, W.32, D.35, G.163, D.165, Y.349, W.350, W.355, E.393 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.35, A:G.163, A:Y.349, A:Y.349 Water bridges: A:W.32, A:D.165, A:R.198 TRS.7: 9 residues within 4Å: Chain B: Y.28, W.32, D.35, G.163, D.165, Y.349, W.350, W.355, E.393 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.35, B:G.163, B:Y.349, B:Y.349 Water bridges: B:W.32, B:D.165, B:R.198 TRS.12: 9 residues within 4Å: Chain C: Y.28, W.32, D.35, G.163, D.165, Y.349, W.350, W.355, E.393 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.35, C:G.163, C:Y.349, C:Y.349 Water bridges: C:W.32, C:D.165, C:R.198

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

MPD.3: 6 residues within 4Å: Chain A: V.190, K.191, H.192, V.193, N.194, P.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.193 Water bridges: A:N.194 MPD.4: 7 residues within 4Å: Chain A: Q.63, G.64, P.65, G.67, P.133, K.134, A.137 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.133, A:A.137 Hydrogen bonds: A:K.134 Water bridges: A:K.134 MPD.5: 7 residues within 4Å: Chain A: L.41, T.109, Y.113, R.243, W.360, E.364 Chain B: R.279 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.41, A:T.109, A:Y.113, A:W.360, B:R.279 Hydrogen bonds: A:R.243 Water bridges: A:T.109, A:R.243, A:D.247 MPD.8: 6 residues within 4Å: Chain B: V.190, K.191, H.192, V.193, N.194, P.195 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.193 Water bridges: B:N.194 MPD.9: 7 residues within 4Å: Chain B: Q.63, G.64, P.65, G.67, P.133, K.134, A.137 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.133, B:A.137 Hydrogen bonds: B:K.134 Water bridges: B:K.134 MPD.10: 7 residues within 4Å: Chain B: L.41, T.109, Y.113, R.243, W.360, E.364 Chain C: R.279 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.41, B:T.109, B:Y.113, B:W.360, C:R.279 Hydrogen bonds: B:R.243 Water bridges: B:T.109, B:R.243, B:D.247 MPD.13: 6 residues within 4Å: Chain C: V.190, K.191, H.192, V.193, N.194, P.195 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.193 Water bridges: C:N.194 MPD.14: 7 residues within 4Å: Chain C: Q.63, G.64, P.65, G.67, P.133, K.134, A.137 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.133, C:A.137 Hydrogen bonds: C:K.134 Water bridges: C:K.134 MPD.15: 7 residues within 4Å: Chain A: R.279 Chain C: L.41, T.109, Y.113, R.243, W.360, E.364 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.41, C:T.109, C:Y.113, C:W.360, A:R.279 Hydrogen bonds: C:R.243 Water bridges: C:T.109, C:R.243, C:D.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazaki, T. et al., Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8. J.Struct.Biol. (2015)

Release Date

2015-03-11

Peptides

Uncharacterized protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Uncharacterized protein

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