SMTL ID : 1qfx.1

PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: G.143, Y.171, N.172, T.175, N.176 Chain C: C.109, Y.110, P.450, I.451, A.452, C.453 6 PLIP interactions: 6 interactions with chain C Water bridges: C:C.453, C:C.453, C:N.107, C:C.453, C:C.453 Hydrophobic interactions: C:Y.110 Hydrogen bonds: C:I.451, C:I.451 NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 11 residues within 4Å: Chain A: C.109, Y.110, P.450, I.451, A.452, C.453 Chain C: G.143, Y.171, N.172, T.175, N.176 6 PLIP interactions: 6 interactions with chain A Water bridges: A:C.453, A:C.453, A:N.107, A:C.453, A:C.453 Hydrophobic interactions: A:Y.110 Hydrogen bonds: A:I.451, A:I.451

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN.2: 13 residues within 4Å: Chain B: G.143, E.144, Y.171, N.172, T.175, N.176 Chain D: N.107, C.109, Y.110, P.450, I.451, A.452, C.453 5 PLIP interactions: 5 interactions with chain D Water bridges: D:C.453, D:C.453 Hydrophobic interactions: D:Y.110 Hydrogen bonds: D:N.107, D:I.451, D:I.451 NAG-NAG-BMA-MAN-MAN.25: 13 residues within 4Å: Chain B: N.107, C.109, Y.110, P.450, I.451, A.452, C.453 Chain D: G.143, E.144, Y.171, N.172, T.175, N.176 5 PLIP interactions: 5 interactions with chain B Water bridges: B:C.453, B:C.453 Hydrophobic interactions: B:Y.110 Hydrogen bonds: B:N.107, B:I.451, B:I.451

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 7 residues within 4Å: Chain A: N.296, A.297, T.300, Y.431, L.432, W.436 Ligands: GOL.12 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.300, A:L.432, A:L.432 Water bridges: A:N.296, A:N.296, A:N.296, A:N.296, A:N.296 NAG.4: 5 residues within 4Å: Chain A: N.180, I.181, N.437, Y.438, N.439 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.439, A:N.439 Water bridges: A:I.181 NAG.13: 7 residues within 4Å: Chain B: N.296, A.297, T.300, Y.431, L.432, W.436 Ligands: GOL.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.300, B:L.432, B:L.432 NAG.14: 4 residues within 4Å: Chain B: N.180, I.181, N.437, N.439 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.439 Water bridges: B:I.181 NAG.26: 7 residues within 4Å: Chain C: N.296, A.297, T.300, Y.431, L.432, W.436 Ligands: GOL.35 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.432, C:L.432 Water bridges: C:N.296, C:N.296, C:N.296, C:N.296, C:N.296 NAG.27: 5 residues within 4Å: Chain C: N.180, I.181, N.437, Y.438, N.439 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.439, C:N.439 Water bridges: C:I.181, C:T.441 NAG.36: 7 residues within 4Å: Chain D: N.296, A.297, T.300, Y.431, L.432, W.436 Ligands: GOL.46 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.432, D:L.432 NAG.37: 4 residues within 4Å: Chain D: N.180, I.181, N.437, N.439 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.439 Water bridges: D:I.181

22 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: G.305, P.306, K.307, R.365 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.66, P.68, S.69, A.72, F.246 Ligand excluded by PLIP SO4.7: 7 residues within 4Å: Chain A: P.334, N.335, G.346, N.347, P.348 Chain B: N.335 Ligands: SO4.17 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: S.69, P.70, S.71 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: P.48, C.52, E.53, V.54, H.139 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: G.305, P.306, K.307, R.365 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: R.66, P.68, S.69, A.72, F.246 Ligand excluded by PLIP SO4.17: 7 residues within 4Å: Chain A: N.335 Chain B: P.334, N.335, G.346, N.347, P.348 Ligands: SO4.7 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: S.69, P.70, S.71 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain B: P.48, C.52, E.53, V.54, H.139 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: S.409, N.412 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: G.305, P.306, K.307, R.365 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain C: R.66, P.68, S.69, A.72, F.246 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain C: P.334, N.335, G.346, N.347, P.348 Chain D: N.335 Ligands: SO4.40 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: S.69, P.70, S.71 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain C: P.48, C.52, E.53, V.54, H.139 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain D: G.305, P.306, K.307, R.365 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain D: R.66, P.68, S.69, A.72, F.246 Ligand excluded by PLIP SO4.40: 7 residues within 4Å: Chain C: N.335 Chain D: P.334, N.335, G.346, N.347, P.348 Ligands: SO4.30 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain D: S.69, P.70, S.71 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain D: P.48, C.52, E.53, V.54, H.139 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain D: S.409, N.412 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: Y.154, R.156, E.184, H.318 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.156 Water bridges: A:Y.154, A:Y.154 GOL.11: 6 residues within 4Å: Chain A: L.123, E.159, R.447 Chain C: E.166, G.170, Y.171 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:E.159, A:R.447, A:R.447, C:E.166 Water bridges: A:E.159, A:R.447, C:Y.173 GOL.12: 7 residues within 4Å: Chain A: Q.304, Y.431, L.432, S.433, W.436, N.437 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.304, A:W.436, A:N.437 GOL.21: 4 residues within 4Å: Chain B: Y.154, R.156, E.184, H.318 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.156 GOL.22: 6 residues within 4Å: Chain B: L.123, E.159, R.447 Chain D: E.166, G.170, Y.171 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:E.166, B:E.159, B:R.447 Water bridges: D:Y.173, B:E.159, B:R.447 GOL.23: 1 residues within 4Å: Ligands: NAG.13 No protein-ligand interaction detected (PLIP) GOL.33: 4 residues within 4Å: Chain C: Y.154, R.156, E.184, H.318 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.156 Water bridges: C:Y.154, C:Y.154, C:E.184, C:E.184, C:T.320 GOL.34: 6 residues within 4Å: Chain A: E.166, G.170, Y.171 Chain C: L.123, E.159, R.447 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:E.166, A:E.166, C:E.159, C:R.447, C:R.447 Water bridges: A:Y.127, A:Y.446, C:R.447 GOL.35: 7 residues within 4Å: Chain C: Q.304, Y.431, L.432, S.433, W.436, N.437 Ligands: NAG.26 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.304, C:W.436, C:N.437 GOL.44: 4 residues within 4Å: Chain D: Y.154, R.156, E.184, H.318 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.156 Water bridges: D:Y.154, D:E.184, D:E.184 GOL.45: 6 residues within 4Å: Chain B: E.166, G.170, Y.171 Chain D: L.123, E.159, R.447 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:E.159, D:R.447, B:E.166, B:E.166 Water bridges: D:R.447, B:Y.127, B:Y.446 GOL.46: 1 residues within 4Å: Ligands: NAG.36 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kostrewa, D. et al., Crystal structure of Aspergillus niger pH 2.5 acid phosphatase at 2. 4 A resolution. J.Mol.Biol. (1999)

Release Date

2000-04-19

Peptides

PROTEIN (PH 2.5 ACID PHOSPHATASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PROTEIN (PH 2.5 ACID PHOSPHATASE)