SMTL ID : 1iwb.2 (1 other biounit)

Crystal structure of diol dehydratase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-oligomer

Ligands

2 x B12: COBALAMIN(Non-covalent)

B12.1: 16 residues within 4Å: Chain A: 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 29 PLIP interactions: 28 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.113, A:A.114, A:L.148, A:L.148, A:L.153, A:P.155, A:Y.196 Hydrogen bonds: A:D.112, A:K.135, A:T.137, A:N.150, A:N.150, A:P.155, A:P.155, A:Q.156, A:A.157, A:N.188, A:S.200, A:S.200 Water bridges: A:D.112, A:D.112, A:D.112, A:D.112, A:Q.133, A:Q.133, A:Q.197, A:H.204 Salt bridges: A:K.135 Metal complexes: B12.1 B12.2: 16 residues within 4Å: 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 25 PLIP interactions: 24 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.113, B:A.114, B:L.148, B:L.153, B:L.153, B:P.155, B:P.158, B:Y.196 Hydrogen bonds: B:D.112, B:K.135, B:N.150, B:N.150, B:P.155, B:P.155, B:Q.156, B:A.157, B:S.200, B:S.200 Water bridges: B:D.112, B:D.112, B:Q.133, B:Q.133, B:N.188 Salt bridges: B:K.135 Metal complexes: B12.2

6 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain C: Q.141, E.170, E.221, Q.296, S.362 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.170, C:E.221, C:S.362, H2O.144, H2O.145 K.4: 5 residues within 4Å: Chain C: G.261, S.264, E.265, E.280, C.283 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:G.261, C:S.264, C:E.265, C:E.280 K.5: 5 residues within 4Å: Chain C: L.203, E.205, E.208, T.222, I.223 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:L.203, C:E.205, C:E.208, C:T.222, C:T.222 K.6: 5 residues within 4Å: Chain E: Q.141, E.170, E.221, Q.296, S.362 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.170, E:E.221, E:S.362, H2O.549, H2O.550 K.7: 5 residues within 4Å: Chain E: G.261, S.264, E.265, E.280, C.283 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:G.261, E:S.264, E:E.280, H2O.553, H2O.620 K.8: 4 residues within 4Å: Chain E: L.203, E.205, E.208, T.222 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:L.203, E:E.205, E:E.208, E:T.222, E:T.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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 beta chain: AB
DIOL DEHYDRATASE alpha chain: CE
DIOL DEHYDRATASE gamma chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
A

E
L

D
G

F
M

DIOL DEHYDRATASE beta chain

DIOL DEHYDRATASE alpha chain

DIOL DEHYDRATASE gamma chain

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