SMTL ID : 4udk.1

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-5-1-mer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.171, A:Y.262 Water bridges: A:N.171, A:K.232, A:Y.262 Salt bridges: A:R.170, A:R.188, A:K.232, A:H.251 PO4.7: 7 residues within 4Å: Chain B: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.171, B:Y.262 Water bridges: B:Y.262 Salt bridges: B:R.170, B:R.188, B:K.232, B:H.251 PO4.12: 7 residues within 4Å: Chain C: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.171 Water bridges: C:R.170, C:K.232, C:Y.262 Salt bridges: C:R.170, C:R.188, C:K.232, C:H.251 PO4.17: 7 residues within 4Å: Chain D: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.18 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.171, D:Y.262 Water bridges: D:K.232 Salt bridges: D:R.170, D:R.188, D:K.232, D:H.251 PO4.23: 7 residues within 4Å: Chain E: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.24 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.171, E:Y.262 Water bridges: E:K.232 Salt bridges: E:R.170, E:R.188, E:K.232, E:H.251 PO4.29: 7 residues within 4Å: Chain F: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.30 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.171, F:Y.262 Water bridges: F:N.171, F:K.232 Salt bridges: F:R.170, F:R.188, F:K.232, F:H.251

6 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.2: 10 residues within 4Å: Chain A: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324 Chain C: C.257 Ligands: PO4.1, NDG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.79, A:D.124, A:Y.262, A:D.324 Water bridges: A:R.79, A:D.124, A:H.194, A:K.232 Salt bridges: A:K.232 BMA.8: 10 residues within 4Å: Chain A: C.257 Chain B: F.63, N.64, R.79, Y.262, V.301, F.303, D.324 Ligands: PO4.7, NDG.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.79 Water bridges: B:R.170, B:H.194, B:K.232, B:Y.262, B:D.324, B:D.324 Salt bridges: B:R.170, B:K.232 BMA.13: 10 residues within 4Å: Chain B: C.257 Chain C: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324 Ligands: PO4.12, NDG.14 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.79, C:D.124, C:Y.262, C:D.324 Water bridges: C:R.79, C:D.124, C:H.194, C:K.232 BMA.18: 10 residues within 4Å: Chain D: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324 Chain F: C.257 Ligands: PO4.17, NDG.19 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.79, D:D.124, D:Y.262, D:D.324 Water bridges: D:R.79, D:K.232, D:D.324 Salt bridges: D:K.232 BMA.24: 10 residues within 4Å: Chain D: C.257 Chain E: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324 Ligands: PO4.23, NDG.25 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:R.79, E:D.124, E:Y.262, E:D.324 Water bridges: E:R.79, E:K.232, E:D.324 Salt bridges: E:K.232 BMA.30: 10 residues within 4Å: Chain E: C.257 Chain F: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324 Ligands: PO4.29, NDG.31 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:R.79, F:D.124, F:Y.262 Water bridges: F:R.79, F:R.170, F:K.232, F:D.324, F:D.324

6 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.3: 8 residues within 4Å: Chain A: R.79, M.87, Y.123, R.170, H.194 Chain C: F.223, L.254 Ligands: BMA.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.79, A:R.79 Water bridges: A:R.85, A:D.124, C:C.257 Salt bridges: A:H.194 Hydrophobic interactions: C:F.223 NDG.9: 9 residues within 4Å: Chain A: F.223, L.254 Chain B: R.79, R.85, M.87, Y.123, R.170, H.194 Ligands: BMA.8 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.79, B:R.79 Water bridges: B:R.85, B:D.324, A:C.257 Salt bridges: B:H.194 Hydrophobic interactions: A:F.223 NDG.14: 9 residues within 4Å: Chain B: F.223, L.254 Chain C: R.79, M.87, Y.123, R.170, G.193, H.194 Ligands: BMA.13 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.223 Water bridges: B:C.257, C:R.85, C:D.124 Hydrogen bonds: C:R.79, C:R.79 Salt bridges: C:H.194 NDG.19: 9 residues within 4Å: Chain D: R.79, R.85, M.87, Y.123, R.170, H.194 Chain F: F.223, L.254 Ligands: BMA.18 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:R.79, D:R.79, D:H.194 Water bridges: D:R.85, D:Y.123, F:C.257 Salt bridges: D:H.194 Hydrophobic interactions: F:F.223 NDG.25: 9 residues within 4Å: Chain D: F.223, L.254 Chain E: R.79, R.85, M.87, Y.123, R.170, H.194 Ligands: BMA.24 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:F.223 Water bridges: D:C.257, E:R.85, E:Y.123 Hydrogen bonds: E:R.79, E:R.79, E:H.194 Salt bridges: E:H.194 NDG.31: 9 residues within 4Å: Chain E: F.223, L.254 Chain F: R.79, M.87, Y.123, R.170, H.194 Ligands: BMA.30, EDO.32 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.79, F:R.79, F:H.194 Water bridges: F:R.85, F:Y.123, E:C.257 Salt bridges: F:H.194 Hydrophobic interactions: E:F.223

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain A: H.143, F.168, N.192 Chain E: F.197, D.199 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.192 PGE.20: 5 residues within 4Å: Chain D: R.133, Y.135, L.161, D.207, M.208 No protein-ligand interaction detected (PLIP) PGE.26: 5 residues within 4Å: Chain A: F.197 Chain E: H.143, G.144, F.168, N.192 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Water bridges: A:G.198, A:D.199, E:N.192 Hydrogen bonds: E:N.192

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

EDO.5: 3 residues within 4Å: Chain A: R.133, Y.135, L.161 No protein-ligand interaction detected (PLIP) EDO.21: 3 residues within 4Å: Chain D: H.194 Chain F: H.255, C.257 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:C.257 EDO.28: 4 residues within 4Å: Chain E: R.133, Y.135, D.207, M.208 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.133, E:Y.135 EDO.32: 4 residues within 4Å: Chain E: F.223 Chain F: G.193, H.194 Ligands: NDG.31 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.194 Water bridges: F:Y.121, F:Y.123 EDO.34: 3 residues within 4Å: Chain F: R.133, Y.135, D.207 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.133, F:Y.135

6 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain A: H.216, V.217, W.275 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.217, A:W.275, H2O.5, H2O.6 K.11: 3 residues within 4Å: Chain B: H.216, V.217, W.275 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.216, B:V.217, B:W.275, H2O.14, H2O.15 K.16: 3 residues within 4Å: Chain C: H.216, V.217, W.275 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:V.217, C:W.275, H2O.23, H2O.24 K.22: 3 residues within 4Å: Chain D: H.216, V.217, W.275 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:W.275, H2O.30, H2O.31 K.27: 3 residues within 4Å: Chain E: H.216, V.217, W.275 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.216, E:V.217, E:W.275, H2O.38, H2O.38 K.33: 3 residues within 4Å: Chain F: H.216, V.217, W.275 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:V.217, F:W.275, H2O.44, H2O.45

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain B: Y.135, Y.151, D.207, M.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.135 GOL.15: 5 residues within 4Å: Chain C: R.133, Y.135, Y.151, D.207, M.208 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.133 Water bridges: C:R.133, C:Y.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ladeveze, S. et al., Structural Bases for N-Glycan Processing by Mannoside Phosphorylase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-05-27

Peptides

UHGB_MP: ABCDF
UHGB_MP: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

E
E

UHGB_MP

UHGB_MP

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