SMTL ID : 1up6.1 (1 other biounit)

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: I.7, G.8, G.10, S.11, Y.13, Y.36, D.37, I.38, D.39, K.42, Q.79, F.80, R.81, L.85, E.104, I.120, Y.124, F.139, T.140, N.141, L.162, C.163, N.164, E.270 Ligands: MN.2, G6P.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.10, A:I.38, A:F.80, A:R.81, A:R.81, A:E.104, A:Y.124, A:F.139, A:N.141, A:N.141, A:N.164, A:N.164 Water bridges: A:Y.13, A:R.81, A:G.83, A:Y.124 Salt bridges: A:K.42, A:R.81, A:R.81 NAD.7: 25 residues within 4Å: Chain C: G.8, G.10, S.11, Y.13, Y.36, D.37, I.38, D.39, K.42, Q.79, F.80, R.81, P.82, E.104, I.120, Y.124, F.139, T.140, N.141, L.162, C.163, N.164, E.270 Ligands: MN.8, G6P.9 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.13 Hydrogen bonds: C:G.10, C:I.38, C:D.39, C:F.80, C:R.81, C:L.85, C:E.104, C:Y.124, C:F.139, C:N.141, C:N.141, C:N.164, C:N.164, C:E.270 Water bridges: C:G.83, C:E.270 Salt bridges: C:K.42, C:R.81, C:R.81

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: C.163, N.164, H.193 Ligands: NAD.1, G6P.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.163, A:H.193 MN.4: 4 residues within 4Å: Chain A: I.38, D.39, E.40 Ligands: MN.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.38, H2O.6 MN.5: 3 residues within 4Å: Chain A: I.38, D.39 Ligands: MN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.38 MN.8: 5 residues within 4Å: Chain C: C.163, N.164, H.193 Ligands: NAD.7, G6P.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.163, C:H.193

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

G6P.3: 14 residues within 4Å: Chain A: Y.13, R.88, E.104, N.141, C.163, N.164, V.165, H.193, Y.242, R.262, V.266, G.291 Ligands: NAD.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.13, A:E.104, A:N.141, A:N.164 Water bridges: A:R.81 Salt bridges: A:R.88, A:R.262 G6P.9: 13 residues within 4Å: Chain C: Y.13, R.88, E.104, N.141, C.163, N.164, V.165, H.193, Y.242, R.262, V.266 Ligands: NAD.7, MN.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.13, C:R.81, C:E.104, C:N.141, C:N.164 Salt bridges: C:R.88, C:R.262

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

SO4.6: 4 residues within 4Å: Chain A: E.249 Chain B: P.390, G.392, D.394 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.390, B:D.394, A:E.249 SO4.10: 5 residues within 4Å: Chain C: E.249 Chain D: E.249, P.390, G.392, D.394 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yip, V.L. et al., An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps by a Family 4 Beta-Glycosidase from Thermotoga Maritima. J.Am.Chem.Soc. (2004)

Release Date

2004-08-02

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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