SMTL ID : 1uc4.1

Structure of diol dehydratase complexed with (S)-1,2-propanediol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 5 residues within 4Å: Chain A: G.261, S.264, E.265, E.280, C.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.261, A:E.265 Water bridges: A:S.264 NH4.2: 6 residues within 4Å: Chain A: L.203, E.205, E.208, T.222, I.223 Ligands: CNC.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.222, A:T.222 NH4.6: 5 residues within 4Å: Chain D: G.261, S.264, E.265, E.280, C.283 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.261, D:E.280, D:E.280 Water bridges: D:S.264 NH4.7: 5 residues within 4Å: Chain D: L.203, E.205, E.208, T.222 Ligands: CNC.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.203, D:E.208

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: Q.141, H.143, E.170, E.221, Q.296, S.362 Ligands: PGO.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.170, A:E.221, A:S.362 K.8: 7 residues within 4Å: Chain D: Q.141, H.143, E.170, E.221, Q.296, S.362 Ligands: PGO.9 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.170, D:E.221, D:S.362

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 12 residues within 4Å: Chain A: H.143, E.170, E.221, T.222, Q.296, V.300, S.301, D.335, Q.336, S.362, F.374 Ligands: K.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.300, A:Q.336, A:F.374 Hydrogen bonds: A:E.170, A:Q.296, A:Q.296 PGO.9: 12 residues within 4Å: Chain D: H.143, E.170, E.221, T.222, Q.296, V.300, S.301, D.335, Q.336, S.362, F.374 Ligands: K.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.300, D:Q.336, D:F.374 Hydrogen bonds: D:E.170, D:E.221, D:Q.296, D:Q.296, D:D.335

2 x CNC: CYANOCOBALAMIN(Non-covalent)

CNC.5: 34 residues within 4Å: Chain A: T.172, V.173, S.202, E.205, T.222, S.224, Y.226, D.234, G.235, 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: NH4.2 41 PLIP interactions: 26 interactions with chain B, 14 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.113, B:A.114, B:L.153, B:L.153, B:P.155, B:P.158, B:Y.196, A:Y.226, A:Q.267, A:A.375 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:E.205, A:E.205, A:S.224, A:Q.267, A:M.373, A:A.375 Water bridges: B:D.112, B:D.112, B:D.112, B:Q.133, B:Q.133, B:Q.133, B:Q.197, A:V.173, A:V.173, A:E.205, A:Y.226 Salt bridges: B:K.135 Metal complexes: CNC.5 CNC.10: 37 residues within 4Å: Chain D: T.172, V.173, A.174, A.176, S.202, L.203, E.205, T.222, S.224, Y.226, D.234, G.235, 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: NH4.7 37 PLIP interactions: 25 interactions with chain E, 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: E:V.113, E:A.114, E:L.148, E:L.148, E:L.153, E:L.153, E:P.155, E:P.158, E:Y.196, D:Y.226, D:Q.267 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:Q.267, D:M.373, D:A.375 Water bridges: E:D.112, E:Q.133, E:Q.133, E:Q.197, E:H.204, D:E.205 Salt bridges: E:K.135 Metal complexes: CNC.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, N. et al., Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase. J.BIOL.CHEM. (2003)

Release Date

2003-07-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
L

B
B

E
E

C
G

F
M

diol dehydrase alpha subunit

diol dehydrase beta subunit

diol dehydrase gamma subunit

Related Entries With Identical Sequence