SMTL ID : 1up7.1 (1 other biounit)

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with NAD and glucose-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 24 residues within 4Å: Chain A: G.9, G.11, S.12, Y.14, Y.37, D.38, I.39, D.40, K.43, Q.80, F.81, R.82, L.86, E.105, I.121, Y.125, F.140, T.141, N.142, E.271, R.291, G.293, Y.296 Ligands: G6P.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.14, A:Y.14 Hydrogen bonds: A:G.11, A:G.11, A:S.12, A:S.12, A:I.39, A:F.81, A:R.82, A:R.82, A:E.105, A:Y.125, A:N.142, A:N.142 Water bridges: A:D.40, A:D.40 Salt bridges: A:K.43, A:R.82, A:R.82, A:R.291 pi-Stacking: A:Y.296 NAD.4: 24 residues within 4Å: Chain B: I.8, G.9, G.11, S.12, Y.14, Y.37, D.38, I.39, D.40, K.43, Q.80, F.81, R.82, E.105, I.121, Y.125, F.140, T.141, N.142, E.271, R.291, G.293, Y.296 Ligands: G6P.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.14, B:Y.14, B:Y.296, B:Y.296, B:Y.296 Hydrogen bonds: B:G.11, B:G.11, B:S.12, B:S.13, B:I.39, B:Q.80, B:F.81, B:R.82, B:R.82, B:E.105, B:Y.125, B:Y.125, B:N.142, B:N.142 Salt bridges: B:K.43, B:R.82, B:R.82, B:R.291 NAD.6: 24 residues within 4Å: Chain C: I.8, G.9, G.11, S.12, Y.14, Y.37, D.38, I.39, D.40, K.43, Q.80, F.81, R.82, E.105, I.121, Y.125, F.140, T.141, N.142, E.271, R.291, G.293, Y.296 Ligands: G6P.7 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:Y.14, C:Y.14 Hydrogen bonds: C:G.11, C:G.11, C:S.12, C:S.12, C:I.39, C:K.43, C:Q.80, C:F.81, C:R.82, C:R.82, C:R.82, C:E.105, C:Y.125, C:N.142, C:N.142, C:E.271 Salt bridges: C:K.43, C:R.82, C:R.82, C:R.291 pi-Stacking: C:Y.296 NAD.9: 25 residues within 4Å: Chain D: G.9, G.11, S.12, S.13, Y.14, Y.37, D.38, I.39, D.40, K.43, Q.80, F.81, R.82, E.105, I.121, Y.125, F.140, T.141, N.142, E.271, R.291, G.293, Y.296, S.297 Ligands: G6P.10 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:Y.14, D:Y.14, D:Y.296 Hydrogen bonds: D:G.11, D:S.12, D:S.12, D:S.13, D:I.39, D:Q.80, D:F.81, D:R.82, D:R.82, D:R.82, D:E.105, D:Y.125, D:Y.125, D:N.142, D:N.142, D:R.291, D:R.291, D:S.297 Salt bridges: D:K.43, D:R.82, D:R.82 pi-Stacking: D:Y.296

4 x G6P: 6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G6P.2: 15 residues within 4Å: Chain A: Y.14, R.89, E.105, N.142, C.164, N.165, V.166, H.194, Y.243, R.263, V.267, R.291, G.292, Y.296 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.14, A:N.142, A:N.165, A:G.292, A:Y.296 Salt bridges: A:R.89, A:R.263, A:R.291 G6P.5: 14 residues within 4Å: Chain B: R.89, E.105, N.142, C.164, N.165, V.166, H.194, Y.243, R.263, V.267, R.291, G.292, Y.296 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.14, B:N.142, B:N.165, B:Y.243, B:G.292, B:Y.296, B:Y.296 Salt bridges: B:R.89, B:R.263, B:R.291 G6P.7: 15 residues within 4Å: Chain C: Y.14, R.89, E.105, N.142, C.164, N.165, V.166, H.194, Y.243, R.263, V.267, R.291, G.292, Y.296 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.14, C:R.82, C:N.142, C:G.292 Salt bridges: C:R.89, C:R.263, C:R.291 G6P.10: 16 residues within 4Å: Chain D: Y.14, R.89, E.105, N.142, C.164, N.165, V.166, H.194, Y.243, R.263, V.267, R.291, G.292, G.293, Y.296 Ligands: NAD.9 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.142, D:N.165, D:N.165, D:Y.243, D:G.292, D:Y.296, D:Y.296 Salt bridges: D:R.89, D:R.263, D:R.291

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: E.250, P.391, G.393, D.395 Chain B: E.250 No protein-ligand interaction detected (PLIP) SO4.8: 5 residues within 4Å: Chain C: E.250, P.391, L.392, G.393 Chain D: E.250 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varrot, A. et al., Nad+ and Metal-Ion Dependent Hydrolysis by Family 4 Glycosidases: Structural Insight Into Specificity for Phospho-Beta-D-Glucosides. J.Mol.Biol. (2005)

Release Date

2004-11-18

Peptides

6-PHOSPHO-BETA-GLUCOSIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

6-PHOSPHO-BETA-GLUCOSIDASE

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