SMTL ID : 4udi.1

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 Angstrom from unknown human gut bacteria (Uhgb_MP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.171, A:Y.262 Water bridges: A:R.170, A:N.171 Salt bridges: A:R.170, A:R.188, A:K.232, A:H.251 PO4.15: 7 residues within 4Å: Chain B: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.171, B:Y.262, B:Y.262 Salt bridges: B:R.170, B:R.188, B:K.232, B:H.251 PO4.26: 7 residues within 4Å: Chain C: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.27 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 PO4.41: 7 residues within 4Å: Chain D: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.42 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.171, D:Y.262, D:Y.262 Water bridges: D:N.171 Salt bridges: D:R.170, D:R.188, D:K.232, D:H.251 PO4.48: 7 residues within 4Å: Chain E: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.49 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 PO4.55: 7 residues within 4Å: Chain F: R.170, N.171, R.188, K.232, H.251, Y.262 Ligands: GOL.56 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.171, F:Y.262 Water bridges: F:R.170, F:N.171 Salt bridges: F:R.170, F:R.188, F:K.232, F:H.251

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.262, V.301, F.303, D.324 Ligands: PO4.1 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: D.40, V.41, P.283, Y.284, L.285, F.340 Chain B: T.83 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: Y.121, G.144, P.145, F.168, N.192 Chain C: F.223 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: Y.284, A.287, R.289 Chain B: R.53, D.54, S.59, N.60, T.83 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: Y.262, V.301, F.303, D.324 Ligands: PO4.15 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: D.40, V.41, P.283, Y.284, F.340 Chain C: T.83 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: Y.135, Y.151, L.161, D.207, M.208 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: F.223 Chain B: Y.121, G.144, P.145, F.168, N.192 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: R.88, L.107, K.108, W.119 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: Y.284, A.287, R.289 Chain C: R.53, D.54, S.59, N.60, T.83 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: Y.262, V.301, F.303, D.324 Ligands: PO4.26 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: T.83 Chain C: D.40, V.41, P.283, Y.284, L.285, F.340 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain C: Y.135, F.183, D.207, M.208 Ligands: EDO.36 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain B: F.223 Chain C: Y.121, G.144, P.145, F.168, N.192 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: R.88, L.107, K.108, W.119 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain A: R.53, D.54, S.59, N.60, T.83 Chain C: Y.284, A.287, R.289 Ligands: EDO.34 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain D: Y.262, F.303, D.324 Ligands: PO4.41 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain D: D.40, V.41, L.42, Y.284, L.285, F.340 Chain E: T.83 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain D: R.133, Y.135, Y.151, D.207, M.208 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain D: Y.121, G.144, P.145, F.168, N.192 Chain F: F.223 Ligand excluded by PLIP GOL.49: 5 residues within 4Å: Chain E: Y.262, V.301, F.303, D.324 Ligands: PO4.48 Ligand excluded by PLIP GOL.50: 6 residues within 4Å: Chain D: F.223 Chain E: Y.121, G.144, P.145, F.168, N.192 Ligand excluded by PLIP GOL.56: 5 residues within 4Å: Chain F: Y.262, V.301, F.303, D.324 Ligands: PO4.55 Ligand excluded by PLIP GOL.57: 8 residues within 4Å: Chain D: T.83 Chain F: D.40, V.41, P.283, Y.284, L.285, F.340 Ligands: GOL.61 Ligand excluded by PLIP GOL.58: 6 residues within 4Å: Chain E: F.223 Chain F: Y.121, G.144, P.145, F.168, N.192 Ligand excluded by PLIP GOL.60: 4 residues within 4Å: Chain F: R.88, L.107, K.108, W.119 Ligand excluded by PLIP GOL.61: 9 residues within 4Å: Chain D: R.53, D.54, S.59, N.60, T.83 Chain F: Y.284, A.287, R.289 Ligands: GOL.57 Ligand excluded by PLIP

6 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: H.216, V.217, W.275 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.216, A:V.217, A:W.275, H2O.5, H2O.6, H2O.8 K.20: 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.15 K.31: 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.22, H2O.23 K.46: 3 residues within 4Å: Chain D: H.216, V.217, W.275 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.216, D:V.217, D:W.275, H2O.29, H2O.30 K.51: 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.35, H2O.36 K.59: 3 residues within 4Å: Chain F: H.216, V.217, W.275 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.216, F:V.217, F:W.275, H2O.40, H2O.40

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

EDO.7: 8 residues within 4Å: Chain A: N.60, S.61, F.63, R.79, D.81, R.85, D.297, D.324 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: E.131, R.177, K.178 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: P.291, M.295 Chain C: R.289 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: S.84, R.86 Chain C: V.225, G.282, P.283, I.346 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.54, L.56, P.57 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: D.113, Q.160, E.162 Chain E: R.213 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: Y.135 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: E.131, R.177, K.178 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: V.225, G.282, P.283, I.346 Chain B: S.84, R.86 Ligand excluded by PLIP EDO.34: 9 residues within 4Å: Chain A: R.53, N.60, R.85, D.297 Chain C: Y.284, A.287, P.288, R.289 Ligands: GOL.33 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: E.131, R.177, K.178 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: E.131, K.178, F.183 Ligands: GOL.29 Ligand excluded by PLIP EDO.38: 1 residues within 4Å: Chain C: R.86 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain C: T.242, P.243, N.311, G.314, I.334 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain B: R.289 Chain C: R.53 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain D: F.129, I.130, E.131, P.176, R.177 Ligand excluded by PLIP EDO.52: 2 residues within 4Å: Chain E: Y.135, M.208 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain E: L.107, K.108, W.119 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain A: R.213 Chain E: C.111, Q.160, L.161, E.162 Ligand excluded by PLIP EDO.62: 8 residues within 4Å: Chain F: N.60, S.61, F.63, R.79, D.81, R.85, D.297, D.324 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain C: R.213 Chain F: C.111, D.112, D.113, Q.160, E.162 Ligand excluded by PLIP

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

PGE.9: 5 residues within 4Å: Chain A: V.68, P.69, C.128, F.129, I.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.129 Water bridges: A:A.307, A:A.307 PGE.24: 5 residues within 4Å: Chain B: V.68, P.69, C.128, F.129, Y.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.129 Water bridges: B:Y.134 PGE.37: 4 residues within 4Å: Chain C: V.68, P.69, C.128, F.129 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.129

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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