SMTL ID : 4udj.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 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: BMA.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.171 Water bridges: A:Y.262 Salt bridges: A:R.170, A:R.188, A:K.232, A:H.251 PO4.11: 7 residues within 4Å: Chain B: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.12 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 PO4.18: 7 residues within 4Å: Chain C: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.171 Salt bridges: C:R.170, C:R.188, C:K.232, C:H.251 PO4.23: 7 residues within 4Å: Chain D: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.24 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.171, D:Y.262 Salt bridges: D:R.170, D:R.188, D:K.232, D:H.251 PO4.30: 7 residues within 4Å: Chain E: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.31 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.171, E:Y.262 Salt bridges: E:R.170, E:R.188, E:K.232, E:H.251 PO4.35: 7 residues within 4Å: Chain F: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: BMA.36 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.171, F:Y.262 Salt bridges: F:R.170, F:R.188, F:K.232, F:H.251

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

BMA.2: 11 residues within 4Å: Chain A: N.64, R.79, Y.123, D.124, R.170, Y.262, V.298, F.303, D.324 Chain C: C.257 Ligands: PO4.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.64, A:R.79, A:D.124, A:D.124, A:R.170 Water bridges: A:K.232, A:D.324 Salt bridges: A:R.170, A:K.232 BMA.12: 12 residues within 4Å: Chain A: C.257 Chain B: N.64, R.79, Y.123, D.124, R.170, N.171, Y.262, V.298, F.303, D.324 Ligands: PO4.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.64, B:R.79, B:D.124, B:D.124, B:R.170 Water bridges: B:K.232 Salt bridges: B:R.170, B:K.232 BMA.19: 10 residues within 4Å: Chain B: C.257 Chain C: N.64, R.79, D.124, R.170, Y.262, V.298, F.303, D.324 Ligands: PO4.18 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.64, C:R.79, C:D.124, C:D.124, C:R.170 Water bridges: C:N.64, C:K.232, C:D.324 Salt bridges: C:R.170, C:K.232 BMA.24: 12 residues within 4Å: Chain D: N.64, R.79, Y.123, D.124, R.170, N.171, Y.262, V.298, F.303, D.324 Chain F: C.257 Ligands: PO4.23 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.64, D:R.79, D:D.124, D:R.170 Water bridges: D:N.64, D:K.232, D:D.324 Salt bridges: D:R.170, D:K.232 BMA.31: 11 residues within 4Å: Chain D: C.257 Chain E: N.64, R.79, D.124, R.170, N.171, Y.262, V.298, F.303, D.324 Ligands: PO4.30 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.64, E:R.79, E:D.124, E:R.170 Water bridges: E:K.232 Salt bridges: E:R.170, E:K.232 BMA.36: 11 residues within 4Å: Chain E: C.257 Chain F: N.64, R.79, Y.123, D.124, R.170, Y.262, V.298, F.303, D.324 Ligands: PO4.35 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.64, F:R.79, F:D.124, F:R.170 Water bridges: F:H.194, F:K.232 Salt bridges: F:R.170, F:K.232

8 x K: POTASSIUM ION(Non-covalent)

K.3: 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.8: 6 residues within 4Å: Chain A: N.60, S.61, F.63, R.85, D.297, D.324 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.61, A:D.297, A:D.324, H2O.7 K.9: 6 residues within 4Å: Chain F: N.60, S.61, F.63, R.85, D.297, D.324 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.61, F:D.297, F:D.324, H2O.44 K.13: 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.13, H2O.14 K.20: 3 residues within 4Å: Chain C: H.216, V.217, W.275 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.216, C:V.217, C:W.275, H2O.21, H2O.22 K.25: 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.29, H2O.29 K.32: 3 residues within 4Å: Chain E: H.216, V.217, W.275 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:W.275, H2O.36 K.37: 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.43, H2O.44

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

EDO.4: 3 residues within 4Å: Chain A: D.54, L.56, P.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.56 EDO.5: 5 residues within 4Å: Chain A: D.113, Q.160, L.161, E.162 Chain E: R.213 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.213 EDO.15: 6 residues within 4Å: Chain B: F.70, D.72, G.73, F.74, F.93, S.94 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.72, B:D.72, B:G.73, B:S.94, B:S.94 EDO.22: 4 residues within 4Å: Chain C: R.88, L.107, K.108, W.119 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.107, C:F.109 EDO.26: 5 residues within 4Å: Chain D: R.88, P.106, L.107, K.108, W.119 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.106, D:K.108 Water bridges: D:L.107 EDO.27: 6 residues within 4Å: Chain D: F.70, D.72, F.74, F.93, S.94, K.95 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.74, D:S.94 EDO.29: 6 residues within 4Å: Chain B: R.213 Chain D: D.112, D.113, Q.160, L.161, E.162 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:R.213, B:R.213, D:D.112, D:E.162, D:E.162 Water bridges: D:D.112 EDO.33: 4 residues within 4Å: Chain E: R.88, L.107, K.108, W.119 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.107, E:K.108 EDO.34: 2 residues within 4Å: Chain E: Y.135, D.207 No protein-ligand interaction detected (PLIP) EDO.38: 3 residues within 4Å: Chain F: R.133, Y.135, M.208 No protein-ligand interaction detected (PLIP) EDO.39: 5 residues within 4Å: Chain F: P.106, L.107, K.108, E.156, T.157 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:P.106, F:K.108

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

PGE.6: 5 residues within 4Å: Chain A: R.88, P.106, L.107, K.108, W.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.108 Water bridges: A:L.107, A:L.107, A:F.109 PGE.7: 5 residues within 4Å: Chain A: R.133, Y.135, Y.151, L.161, D.207 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.135, A:K.178 PGE.10: 5 residues within 4Å: Chain A: A.47, N.48, P.49, I.50, I.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 PGE.14: 3 residues within 4Å: Chain B: V.46, A.47, N.48 No protein-ligand interaction detected (PLIP) PGE.16: 4 residues within 4Å: Chain B: R.133, Y.135, L.161, D.207 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.207 PGE.17: 4 residues within 4Å: Chain B: D.270, K.276, V.277, K.278 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.276 PGE.21: 4 residues within 4Å: Chain C: R.133, Y.135, Y.151, L.161 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.133, C:R.133 PGE.28: 5 residues within 4Å: Chain D: R.133, Y.135, D.207, M.208, E.209 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.135, D:E.209 PGE.40: 4 residues within 4Å: Chain F: D.270, V.277, K.278, F.279 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.270

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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