SMTL ID : 1mmf.3 (2 other biounits)

Crystal structure of substrate free form of glycerol dehydratase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-oligomer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: Q.142, H.144, E.171, E.222, Q.297, D.336, S.363 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.171, A:E.222, A:S.363, H2O.5 K.2: 5 residues within 4Å: Chain D: Q.142, E.171, E.222, Q.297, S.363 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.171, D:E.222, D:S.363, H2O.121

2 x B12: COBALAMIN(Non-covalent)

B12.3: 34 residues within 4Å: Chain A: T.173, V.174, G.175, A.177, S.203, V.204, E.206, T.223, S.225, D.235, L.268, M.269, S.302, Q.337, M.374, F.375, A.376 Chain B: L.46, D.79, S.81, K.102, T.104, L.115, N.117, L.120, S.122, Q.123, A.124, P.125, V.159, R.160, F.163, M.164, A.167 27 PLIP interactions: 9 interactions with chain A, 17 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.268, A:A.376, B:L.115, B:L.115, B:L.120, B:F.163, B:A.167 Hydrogen bonds: A:T.173, A:A.177, A:S.203, A:E.206, A:S.225, A:M.374, A:A.376, B:D.79, B:K.102, B:T.104, B:N.117, B:N.117, B:S.122, B:S.122, B:S.122, B:Q.123, B:A.124 Water bridges: B:Q.100 Salt bridges: B:K.102 Metal complexes: B12.3 B12.4: 34 residues within 4Å: Chain D: T.173, V.174, S.203, V.204, E.206, T.223, S.225, Y.227, D.235, L.268, M.269, S.302, Q.337, M.374, F.375, A.376 Chain E: L.46, D.79, V.80, S.81, K.102, T.104, V.106, L.115, N.117, L.120, S.122, Q.123, A.124, P.125, V.159, R.160, F.163, A.167 31 PLIP interactions: 10 interactions with chain D, 20 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.173, D:Y.227, D:L.268, D:F.375, E:L.46, E:V.80, E:V.106, E:L.115, E:L.120, E:P.125, E:V.159, E:F.163, E:A.167 Hydrogen bonds: D:E.206, D:S.225, D:M.374, D:A.376, E:D.79, E:K.102, E:N.117, E:S.122, E:S.122, E:Q.123, E:A.124 Water bridges: D:E.206, D:L.268, E:D.79, E:H.171, E:H.171 Salt bridges: E:K.102 Metal complexes: B12.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, D.I. et al., Crystal structure of substrate free form of glycerol dehydratase. J.Inorg.Biochem. (2003)

Release Date

2003-06-10

Peptides

glycerol dehydrase alpha subunit: AD
glycerol dehydrase beta subunit: BE
glycerol dehydrase gamma subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
L

B
B

E
E

C
G

F
M

glycerol dehydrase alpha subunit

glycerol dehydrase beta subunit

glycerol dehydrase gamma subunit

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