SMTL ID : 1ta9.1

Crystal structure of glycerol dehydrogenase from Schizosaccharomyces pombe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.182, D.232, H.315, H.333 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.232, A:D.232, A:H.315, A:H.333 ZN.7: 5 residues within 4Å: Chain B: D.182, D.232, H.315, H.333 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.232, B:D.232, B:H.315, B:H.333 ZN.10: 5 residues within 4Å: Chain C: D.182, D.232, H.315, H.333 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.232, C:D.232, C:H.315, C:H.333 ZN.16: 5 residues within 4Å: Chain D: D.182, D.232, H.315, H.333 Ligands: GOL.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.232, D:D.232, D:H.315, D:H.333 ZN.19: 5 residues within 4Å: Chain E: D.182, D.232, H.315, H.333 Ligands: GOL.23 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.232, E:D.232, E:H.315, E:H.333 ZN.25: 5 residues within 4Å: Chain F: D.182, D.232, H.315, H.333 Ligands: GOL.27 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.232, F:D.232, F:H.315, F:H.333 ZN.28: 5 residues within 4Å: Chain G: D.182, D.232, H.315, H.333 Ligands: GOL.32 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.232, G:D.232, G:H.315, G:H.333 ZN.34: 5 residues within 4Å: Chain H: D.182, D.232, H.315, H.333 Ligands: GOL.36 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.232, H:D.232, H:H.315, H:H.333

8 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.182, A:D.232, A:S.235, A:T.236, H2O.2 K.8: 7 residues within 4Å: Chain B: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.182, B:D.232, H2O.16 K.11: 7 residues within 4Å: Chain C: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.14 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.182, C:D.232, C:S.235, C:T.236, H2O.28 K.17: 7 residues within 4Å: Chain D: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.182, D:D.232, H2O.42 K.20: 7 residues within 4Å: Chain E: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.23 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.182, E:D.232, E:S.235, E:T.236, H2O.54 K.26: 7 residues within 4Å: Chain F: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.27 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.182, F:D.232, H2O.69 K.29: 7 residues within 4Å: Chain G: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.32 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.182, G:D.232, G:S.235, G:T.236, H2O.81 K.35: 7 residues within 4Å: Chain H: D.182, D.232, S.235, T.236, S.302, H.315 Ligands: GOL.36 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.182, H:D.232, H2O.95

8 x ALA: ALANINE(Non-covalent)

ALA.3: 5 residues within 4Å: Chain A: A.130, V.190, I.191, Y.192 Ligands: ALA.4 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: A.4, A:Y.192 Hydrophobic interactions: A:I.191 ALA.4: 4 residues within 4Å: Chain A: A.130, S.131, Y.192 Ligands: ALA.3 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: A.3, A:A.130 Water bridges: A:L.132 ALA.12: 5 residues within 4Å: Chain C: A.130, V.190, I.191, Y.192 Ligands: ALA.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.191 Hydrogen bonds: C:Y.192, A.13 ALA.13: 4 residues within 4Å: Chain C: A.130, S.131, Y.192 Ligands: ALA.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:A.130, A.12 Water bridges: C:L.132 ALA.21: 5 residues within 4Å: Chain E: A.130, V.190, I.191, Y.192 Ligands: ALA.22 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:I.191 Hydrogen bonds: E:Y.192, A.22 ALA.22: 4 residues within 4Å: Chain E: A.130, S.131, Y.192 Ligands: ALA.21 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: E:A.130, A.21 Water bridges: E:L.132 ALA.30: 5 residues within 4Å: Chain G: A.130, V.190, I.191, Y.192 Ligands: ALA.31 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.191 Hydrogen bonds: G:Y.192 ALA.31: 4 residues within 4Å: Chain G: A.130, S.131, Y.192 Ligands: ALA.30 1 PLIP interactions: 1 interactions with chain G Water bridges: G:L.132

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: D.182, Y.201, D.232, F.306, L.311, H.315, H.333 Ligands: ZN.1, K.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.182, A:D.182, A:S.186 GOL.6: 9 residues within 4Å: Chain A: K.162, A.165, L.170, S.172, S.187, Y.204, L.206, N.207, P.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.170, A:L.206 Water bridges: A:L.206 GOL.9: 7 residues within 4Å: Chain B: D.182, D.232, L.311, H.315, H.333 Ligands: ZN.7, K.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.186 GOL.14: 9 residues within 4Å: Chain C: D.182, Y.201, D.232, F.306, L.311, H.315, H.333 Ligands: ZN.10, K.11 3 PLIP interactions: 3 interactions with chain C Water bridges: C:D.182, C:D.182, C:S.186 GOL.15: 9 residues within 4Å: Chain C: K.162, A.165, L.170, S.172, S.187, Y.204, L.206, N.207, P.208 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.170, C:L.206 Water bridges: C:L.206 GOL.18: 7 residues within 4Å: Chain D: D.182, D.232, L.311, H.315, H.333 Ligands: ZN.16, K.17 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.186 GOL.23: 9 residues within 4Å: Chain E: D.182, Y.201, D.232, F.306, L.311, H.315, H.333 Ligands: ZN.19, K.20 3 PLIP interactions: 3 interactions with chain E Water bridges: E:D.182, E:D.182, E:S.186 GOL.24: 9 residues within 4Å: Chain E: K.162, A.165, L.170, S.172, S.187, Y.204, L.206, N.207, P.208 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.170, E:L.206 Water bridges: E:L.206 GOL.27: 7 residues within 4Å: Chain F: D.182, D.232, L.311, H.315, H.333 Ligands: ZN.25, K.26 1 PLIP interactions: 1 interactions with chain F Water bridges: F:S.186 GOL.32: 9 residues within 4Å: Chain G: D.182, Y.201, D.232, F.306, L.311, H.315, H.333 Ligands: ZN.28, K.29 3 PLIP interactions: 3 interactions with chain G Water bridges: G:D.182, G:D.182, G:S.186 GOL.33: 9 residues within 4Å: Chain G: K.162, A.165, L.170, S.172, S.187, Y.204, L.206, N.207, P.208 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:L.170, G:L.206 Water bridges: G:L.206 GOL.36: 7 residues within 4Å: Chain H: D.182, D.232, L.311, H.315, H.333 Ligands: ZN.34, K.35 1 PLIP interactions: 1 interactions with chain H Water bridges: H:S.186

Links

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Citation

Mulichak, A.M., Crystal structure of glycerol dehydrogenase from Schyzosaccharomyces pombe. To be Published

Release Date

2005-08-16

Peptides

glycerol dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

glycerol dehydrogenase