SMTL ID : 3wau.1

Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with M1P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: V.311, G.312, R.315 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:G.312 Water bridges: A:P.310, E:R.346, E:R.346 Salt bridges: A:R.315 PO4.2: 6 residues within 4Å: Chain A: H.15, E.16, L.19, P.47, F.49, R.111 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.15, A:R.111 PO4.5: 3 residues within 4Å: Chain B: V.311, G.312, R.315 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.312 Salt bridges: B:R.315 Water bridges: D:R.346, D:R.346 PO4.6: 6 residues within 4Å: Chain B: H.15, E.16, L.19, P.47, F.49, R.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.16, B:E.16 Water bridges: B:R.111 Salt bridges: B:H.15, B:R.111 PO4.9: 3 residues within 4Å: Chain C: V.311, G.312, R.315 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.312 Water bridges: C:P.310, A:R.346, A:R.346 Salt bridges: C:R.315 PO4.10: 6 residues within 4Å: Chain C: H.15, E.16, L.19, P.47, F.49, R.111 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.15, C:R.111 PO4.13: 3 residues within 4Å: Chain D: V.311, G.312, R.315 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:G.312 Salt bridges: D:R.315 Water bridges: F:R.346, F:R.346 PO4.14: 6 residues within 4Å: Chain D: H.15, E.16, L.19, P.47, F.49, R.111 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.16, D:E.16 Water bridges: D:R.111 Salt bridges: D:H.15, D:R.111 PO4.17: 3 residues within 4Å: Chain E: V.311, G.312, R.315 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.312 Water bridges: E:P.310, C:R.346, C:R.346 Salt bridges: E:R.315 PO4.18: 6 residues within 4Å: Chain E: H.15, E.16, L.19, P.47, F.49, R.111 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:H.15, E:R.111 PO4.21: 3 residues within 4Å: Chain F: V.311, G.312, R.315 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.312 Salt bridges: F:R.315 Water bridges: B:R.346, B:R.346 PO4.22: 6 residues within 4Å: Chain F: H.15, E.16, L.19, P.47, F.49, R.111 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.16, F:E.16 Water bridges: F:R.111 Salt bridges: F:H.15, F:R.111

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

MPD.3: 8 residues within 4Å: Chain A: R.88, E.90, R.94, V.319, D.344 Chain C: R.276, C.278 Ligands: M1P.4 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:D.344 Hydrogen bonds: A:R.88, A:R.94, A:R.94, A:D.344, C:R.276, C:R.276 Water bridges: A:Y.130 MPD.7: 8 residues within 4Å: Chain B: R.88, E.90, R.94, V.319, D.344 Chain F: R.276, C.278 Ligands: M1P.8 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:D.344 Hydrogen bonds: B:R.88, B:R.94, B:R.94, F:R.276, F:R.276 MPD.11: 8 residues within 4Å: Chain C: R.88, E.90, R.94, V.319, D.344 Chain E: R.276, C.278 Ligands: M1P.12 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain C Hydrogen bonds: E:R.276, E:R.276, C:R.88, C:R.94, C:R.94, C:D.344 Hydrophobic interactions: C:D.344 Water bridges: C:Y.130 MPD.15: 8 residues within 4Å: Chain B: R.276, C.278 Chain D: R.88, E.90, R.94, V.319, D.344 Ligands: M1P.16 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:D.344 Hydrogen bonds: D:R.88, D:R.94, D:R.94, B:R.276, B:R.276 MPD.19: 8 residues within 4Å: Chain A: R.276, C.278 Chain E: R.88, E.90, R.94, V.319, D.344 Ligands: M1P.20 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:D.344 Hydrogen bonds: E:R.88, E:R.94, E:R.94, E:D.344, A:R.276, A:R.276 Water bridges: E:Y.130 MPD.23: 8 residues within 4Å: Chain D: R.276, C.278 Chain F: R.88, E.90, R.94, V.319, D.344 Ligands: M1P.24 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:D.344 Hydrogen bonds: F:R.88, F:R.94, F:R.94, D:R.276, D:R.276

6 x M1P: 1-O-phosphono-alpha-D-mannopyranose(Non-covalent)

M1P.4: 13 residues within 4Å: Chain A: N.73, R.88, D.131, R.191, N.192, R.209, K.254, H.273, Y.284, V.319, F.324, D.344 Ligands: MPD.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.73, A:R.88, A:D.131, A:R.191, A:N.192, A:Y.284, A:D.344 Water bridges: A:Y.130, A:R.191, A:R.209, A:Y.284, A:Y.284 Salt bridges: A:R.191, A:R.191, A:R.209, A:K.254, A:H.273 M1P.8: 13 residues within 4Å: Chain B: N.73, R.88, D.131, R.191, N.192, R.209, K.254, H.273, Y.284, V.319, F.324, D.344 Ligands: MPD.7 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:N.73, B:R.88, B:D.131, B:N.192, B:Y.284, B:Y.284, B:D.344 Water bridges: B:R.209, B:R.209, F:A.279 Salt bridges: B:R.191, B:R.209, B:K.254, B:H.273 M1P.12: 13 residues within 4Å: Chain C: N.73, R.88, D.131, R.191, N.192, R.209, K.254, H.273, Y.284, V.319, F.324, D.344 Ligands: MPD.11 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.73, C:R.88, C:D.131, C:R.191, C:N.192, C:Y.284, C:D.344 Water bridges: C:Y.130, C:R.191, C:R.209, C:Y.284, C:Y.284 Salt bridges: C:R.191, C:R.191, C:R.209, C:K.254, C:H.273 M1P.16: 13 residues within 4Å: Chain D: N.73, R.88, D.131, R.191, N.192, R.209, K.254, H.273, Y.284, V.319, F.324, D.344 Ligands: MPD.15 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.73, D:R.88, D:D.131, D:N.192, D:Y.284, D:Y.284, D:D.344 Water bridges: D:R.209, D:R.209, B:A.279 Salt bridges: D:R.191, D:R.209, D:K.254, D:H.273 M1P.20: 13 residues within 4Å: Chain E: N.73, R.88, D.131, R.191, N.192, R.209, K.254, H.273, Y.284, V.319, F.324, D.344 Ligands: MPD.19 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:N.73, E:R.88, E:D.131, E:R.191, E:N.192, E:Y.284, E:D.344 Water bridges: E:Y.130, E:R.191, E:R.209, E:Y.284, E:Y.284 Salt bridges: E:R.191, E:R.191, E:R.209, E:K.254, E:H.273 M1P.24: 13 residues within 4Å: Chain F: N.73, R.88, D.131, R.191, N.192, R.209, K.254, H.273, Y.284, V.319, F.324, D.344 Ligands: MPD.23 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:N.73, F:R.88, F:D.131, F:N.192, F:Y.284, F:Y.284, F:D.344 Water bridges: F:R.209, F:R.209, D:A.279 Salt bridges: F:R.191, F:R.209, F:K.254, F:H.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakae, S. et al., Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP. J.Mol.Biol. (2013)

Release Date

2013-09-04

Peptides

4-O-beta-D-mannosyl-D-glucose phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

4-O-beta-D-mannosyl-D-glucose phosphorylase

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