SMTL ID : 6wbt.1

2.52 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Glucose-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: N.149, C.171, H.201 Ligands: G6P.2, NAD.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.171, A:H.201 MN.4: 4 residues within 4Å: Chain B: N.149, C.171, H.201 Ligands: NAD.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.171, B:H.201 MN.7: 6 residues within 4Å: Chain C: N.149, C.171, N.200, H.201 Ligands: G6P.8, NAD.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.171, C:H.201 MN.12: 5 residues within 4Å: Chain D: N.149, C.171, H.201 Ligands: G6P.13, NAD.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.171, D:H.201

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

G6P.2: 15 residues within 4Å: Chain A: Y.16, R.94, E.110, N.149, C.171, D.172, M.173, H.201, W.244, Y.266, R.286, V.290, R.294 Ligands: MN.1, NAD.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.110, A:N.149, A:D.172, A:Y.266 Water bridges: A:R.87, A:R.87 Salt bridges: A:R.94, A:R.286, A:R.294 G6P.8: 14 residues within 4Å: Chain C: R.94, E.110, N.149, C.171, D.172, M.173, H.201, W.244, Y.266, R.286, V.290, R.294 Ligands: MN.7, NAD.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.149, C:D.172 Salt bridges: C:R.94, C:R.286, C:R.294 G6P.13: 11 residues within 4Å: Chain D: Y.16, R.94, E.110, N.149, D.172, M.173, Y.266, R.286, R.294 Ligands: MN.12, NAD.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.16, D:N.149, D:Y.266 Water bridges: D:E.110 Salt bridges: D:R.94, D:R.286, D:R.294

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

NAD.3: 28 residues within 4Å: Chain A: C.10, G.11, G.13, S.14, T.15, Y.16, Y.39, D.40, I.41, D.42, R.45, Q.85, M.86, R.87, V.88, L.91, E.110, Y.119, P.126, Y.147, N.149, I.170, C.171, D.172, R.294, H.321 Ligands: MN.1, G6P.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.16 Hydrogen bonds: A:G.13, A:G.13, A:G.13, A:T.15, A:T.15, A:Y.16, A:I.41, A:R.87, A:L.91, A:E.110, A:Y.119, A:Y.147, A:N.149, A:N.149, A:D.172, A:D.172 Water bridges: A:Y.39, A:R.87 Salt bridges: A:R.45, A:R.87, A:R.87, A:R.294 NAD.6: 28 residues within 4Å: Chain B: C.10, G.11, G.13, S.14, T.15, Y.16, Y.39, D.40, I.41, D.42, R.45, Q.85, M.86, R.87, V.88, G.90, L.91, E.110, Y.119, P.126, Y.147, S.148, N.149, C.171, D.172, R.294, H.321 Ligands: MN.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.16 Hydrogen bonds: B:G.13, B:G.13, B:T.15, B:T.15, B:Y.16, B:R.87, B:L.91, B:E.110, B:Y.147, B:N.149, B:N.149, B:D.172, B:D.172 Salt bridges: B:R.45, B:R.87, B:R.87, B:R.294 NAD.9: 26 residues within 4Å: Chain C: C.10, G.11, G.13, S.14, T.15, Y.16, D.40, I.41, D.42, R.45, Q.85, M.86, R.87, V.88, L.91, E.110, Y.119, Y.147, S.148, N.149, C.171, D.172, R.294, H.321 Ligands: MN.7, G6P.8 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.16 Hydrogen bonds: C:G.13, C:G.13, C:T.15, C:T.15, C:Y.16, C:R.87, C:R.87, C:E.110, C:Y.119, C:N.149, C:N.149, C:D.172 Water bridges: C:R.45, C:E.295 Salt bridges: C:R.45, C:R.87, C:R.87, C:R.294 NAD.14: 26 residues within 4Å: Chain D: C.10, G.13, S.14, T.15, Y.16, Y.39, D.40, I.41, D.42, R.45, Q.85, M.86, R.87, E.110, Y.119, P.126, Y.147, S.148, N.149, I.170, C.171, D.172, M.173, H.321 Ligands: MN.12, G6P.13 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.16 Hydrogen bonds: D:G.13, D:G.13, D:G.13, D:T.15, D:Y.16, D:R.87, D:L.91, D:E.110, D:N.149, D:N.149, D:I.170, D:D.172 Water bridges: D:D.42, D:D.42 Salt bridges: D:R.45, D:R.87, D:R.87

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain B: R.94, E.110, W.244, R.286, V.290, R.294 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.16, B:Y.16 Water bridges: B:R.94 Salt bridges: B:R.94, B:R.286, B:R.294 PO4.10: 3 residues within 4Å: Chain C: T.206, Y.261, V.375 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.261 Water bridges: C:T.206, C:T.206

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 2 residues within 4Å: Chain D: S.354, D.355 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.355 Water bridges: D:L.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., 2.52 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut Microorganisms in Complex with NAD and Glucose-6-phosphate. To Be Published

Release Date

2021-03-31

Peptides

cellulase IBT99: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

cellulase IBT99