SMTL ID : 4udg.1

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with N-acetylglucosamine and inorganic phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

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: GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.171 Water bridges: A:N.171, 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: GOL.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.171, 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: GOL.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.171 Water bridges: C:R.170 Salt bridges: C:R.170, C:R.188, C:K.232, C:H.251 PO4.16: 7 residues within 4Å: Chain D: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.18 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.171, D:Y.262 Water bridges: D:N.171, D:K.232 Salt bridges: D:R.170, D:R.188, D:K.232, D:H.251 PO4.20: 7 residues within 4Å: Chain E: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.22 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 PO4.26: 7 residues within 4Å: Chain F: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.28 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.171, F:Y.262 Water bridges: F:R.170, F:K.232 Salt bridges: F:R.170, F:R.188, F:K.232, F:H.251

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

NDG.2: 8 residues within 4Å: Chain A: R.79, M.87, Y.123, R.170, H.194 Chain C: F.223, L.254 Ligands: GOL.3 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:F.223 Water bridges: C:C.257, A:R.85 Hydrogen bonds: A:R.79, A:R.79 Salt bridges: A:H.194 NDG.8: 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: GOL.9 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.223 Hydrogen bonds: B:R.79, B:R.79 Water bridges: B:R.85, B:D.324 Salt bridges: B:H.194 NDG.13: 8 residues within 4Å: Chain B: F.223, L.254 Chain C: R.79, M.87, Y.123, R.170, H.194 Ligands: GOL.14 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.324 Hydrogen bonds: C:R.79, C:R.79 Salt bridges: C:H.194 NDG.17: 7 residues within 4Å: Chain D: R.79, M.87, Y.123, R.170, H.194 Chain F: F.223 Ligands: GOL.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.21: 8 residues within 4Å: Chain D: F.223, L.254 Chain E: R.79, M.87, Y.123, R.170, H.194 Ligands: GOL.22 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:R.79, E:R.79, E:H.194 Water bridges: E:R.85, E:Y.123, D:C.257 Salt bridges: E:H.194 Hydrophobic interactions: D:F.223 NDG.27: 8 residues within 4Å: Chain E: F.223 Chain F: R.79, R.85, M.87, Y.123, R.170, H.194 Ligands: GOL.28 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:F.223 Water bridges: E:C.257, F:R.85, F:Y.123 Hydrogen bonds: F:R.79, F:R.79, F:H.194 Salt bridges: F:H.194

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: Y.262, V.298, V.301, F.303, D.324 Chain C: C.257 Ligands: PO4.1, NDG.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.170, A:D.324, A:D.324 GOL.9: 7 residues within 4Å: Chain A: C.257 Chain B: Y.262, V.301, F.303, D.324 Ligands: PO4.7, NDG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.262, B:D.324 GOL.10: 5 residues within 4Å: Chain B: Y.135, Y.151, L.161, D.207, M.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.135 GOL.14: 7 residues within 4Å: Chain B: C.257 Chain C: Y.262, V.301, F.303, D.324 Ligands: PO4.12, NDG.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.324 Water bridges: C:R.170, C:K.232, C:D.324 GOL.18: 7 residues within 4Å: Chain D: Y.262, V.301, F.303, D.324 Chain F: C.257 Ligands: PO4.16, NDG.17 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.170, D:D.324, D:D.324 GOL.22: 8 residues within 4Å: Chain D: C.257 Chain E: Y.262, V.298, V.301, F.303, D.324 Ligands: PO4.20, NDG.21 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.170, E:D.324, E:D.324 GOL.28: 7 residues within 4Å: Chain E: C.257 Chain F: Y.262, V.301, F.303, D.324 Ligands: PO4.26, NDG.27 2 PLIP interactions: 2 interactions with chain F Water bridges: F:G.321, F:D.324

6 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: H.216, V.217, W.275 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.216, 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.16, H2O.17 K.15: 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.27, H2O.28 K.19: 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.36, H2O.36 K.23: 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.45, H2O.45 K.29: 3 residues within 4Å: Chain F: H.216, V.217, W.275 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:W.275, H2O.53, H2O.54

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

EDO.5: 4 residues within 4Å: Chain A: D.113, Q.160, L.161, E.162 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.162 EDO.6: 2 residues within 4Å: Chain A: R.133, Y.135 No protein-ligand interaction detected (PLIP) EDO.24: 2 residues within 4Å: Chain E: Y.135, D.207 No protein-ligand interaction detected (PLIP) EDO.25: 3 residues within 4Å: Chain E: L.107, K.108, W.119 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.107 EDO.30: 4 residues within 4Å: Chain F: R.133, Y.135, D.207, M.208 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.133

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UHGB_MP

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