SMTL ID : 1iwb.1 (1 other biounit)

Crystal structure of diol dehydratase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-2-mer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: Q.141, E.170, E.221, Q.296, S.362 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.170, A:E.221, A:S.362, H2O.1, H2O.1 K.2: 5 residues within 4Å: Chain A: G.261, S.264, E.265, E.280, C.283 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:G.261, A:S.264, A:E.265, A:E.280 K.3: 6 residues within 4Å: Chain A: L.203, E.205, E.208, T.222, I.223 Ligands: B12.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.203, A:E.205, A:E.208, A:T.222, A:T.222 K.5: 5 residues within 4Å: Chain D: Q.141, E.170, E.221, Q.296, S.362 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.170, D:E.221, D:S.362, H2O.20, H2O.20 K.6: 5 residues within 4Å: Chain D: G.261, S.264, E.265, E.280, C.283 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.261, D:S.264, D:E.280, H2O.20, H2O.22 K.7: 5 residues within 4Å: Chain D: L.203, E.205, E.208, T.222 Ligands: B12.8 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:L.203, D:E.205, D:E.208, D:T.222, D:T.222

2 x B12: COBALAMIN(Non-covalent)

B12.4: 34 residues within 4Å: Chain A: T.172, V.173, A.174, S.202, E.205, T.222, S.224, Y.226, D.234, Q.267, M.268, S.301, C.302, Q.336, M.373, F.374, A.375 Chain B: D.112, V.113, A.114, K.135, T.137, L.148, N.150, L.153, P.155, Q.156, A.157, P.158, R.193, Y.196, Q.197, S.200 Ligands: K.3 41 PLIP interactions: 27 interactions with chain B, 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.113, B:A.114, B:L.148, B:L.148, B:L.153, B:P.155, B:Y.196, A:Y.226, A:Q.267 Hydrogen bonds: B:D.112, B:K.135, B:T.137, B:N.150, B:N.150, B:P.155, B:P.155, B:Q.156, B:A.157, B:S.200, B:S.200, A:T.172, A:V.173, A:E.205, A:S.224, A:M.373, A:A.375 Water bridges: B:D.112, B:D.112, B:D.112, B:D.112, B:Q.133, B:Q.133, B:Q.197, B:H.204, A:A.176, A:E.205, A:Y.226, A:Q.267, A:Q.267 Salt bridges: B:K.135 Metal complexes: B12.4 B12.8: 35 residues within 4Å: Chain D: T.172, V.173, A.174, A.176, S.202, E.205, T.222, S.224, Y.226, D.234, Q.267, M.268, S.301, C.302, Q.336, M.373, F.374, A.375 Chain E: D.112, V.113, A.114, K.135, T.137, L.148, N.150, L.153, P.155, Q.156, A.157, P.158, R.193, Y.196, Q.197, S.200 Ligands: K.7 38 PLIP interactions: 24 interactions with chain E, 13 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: E:V.113, E:A.114, E:L.148, E:L.153, E:L.153, E:P.155, E:P.158, E:Y.196, D:Y.226, D:Q.267, D:A.375 Hydrogen bonds: E:D.112, E:K.135, E:N.150, E:N.150, E:P.155, E:P.155, E:Q.156, E:A.157, E:S.200, E:S.200, D:T.172, D:T.172, D:A.176, D:E.205, D:S.224, D:M.373, D:A.375 Water bridges: E:D.112, E:D.112, E:Q.133, E:Q.133, E:Q.197, D:T.222, D:Q.267, D:Q.267 Salt bridges: E:K.135 Metal complexes: B12.8

Links

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Citation

Shibata, N. et al., Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase. Biochemistry (2002)

Release Date

2003-05-01

Peptides

DIOL DEHYDRATASE alpha chain: AD
DIOL DEHYDRATASE beta chain: BE
DIOL DEHYDRATASE gamma chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
L

B
B

E
E

C
G

F
M

DIOL DEHYDRATASE alpha chain

DIOL DEHYDRATASE beta chain

DIOL DEHYDRATASE gamma chain

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