SMTL ID : 1eex.1

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 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.2: 5 residues within 4Å: Chain A: G.261, S.264, E.265, E.280, C.283 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.261, A:S.264, A:E.265, A:E.280, H2O.1 K.5: 6 residues within 4Å: Chain D: Q.141, E.170, E.221, Q.296, S.362 Ligands: PGO.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.170, D:E.221, D:S.362 K.6: 5 residues within 4Å: Chain D: G.261, S.264, E.265, E.280, C.283 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.261, D:S.264, D:E.265, D:E.280, H2O.44

2 x COY: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN(Non-covalent)

COY.3: 37 residues within 4Å: Chain A: T.172, V.173, E.205, T.222, S.224, V.225, Y.226, D.234, T.259, S.260, G.261, S.264, Q.267, M.268, S.299, V.300, S.301, C.302, Q.336, M.373, F.374, A.375 Chain B: D.112, V.113, 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 45 PLIP interactions: 29 interactions with chain B, 15 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.113, B:L.148, B:L.153, B:P.155, B:Y.196, A:T.222, 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:Q.197, B:S.200, B:S.200, A:V.173, A:E.205, A:E.205, A:G.261, A:S.301, A:M.373, A:M.373 Water bridges: B:D.112, B:D.112, B:D.112, B:D.112, B:D.112, B:D.112, B:V.113, B:Q.133, B:Q.133, B:N.150, B:L.153, A:A.176, A:T.222, A:Y.226, A:S.264, A:S.264, A:Q.267 Salt bridges: B:K.135 Metal complexes: COY.3 COY.7: 39 residues within 4Å: Chain D: T.172, V.173, L.203, E.205, T.222, S.224, V.225, Y.226, D.234, T.259, S.260, G.261, S.264, Q.267, M.268, S.299, V.300, 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 42 PLIP interactions: 27 interactions with chain E, 14 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:L.153, E:P.155, E:Y.196, D:T.222, 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:Q.197, E:S.200, D:T.172, D:E.205, D:G.261, D:Q.267, D:S.301, D:M.373, D:M.373 Water bridges: E:D.112, E:D.112, E:D.112, E:D.112, E:Q.133, E:L.153, E:H.204, D:A.176, D:K.242, D:S.264 Salt bridges: E:K.135 Metal complexes: COY.7

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.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.336, A:F.374 Hydrogen bonds: A:E.170, A:Q.296, A:Q.296 PGO.8: 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.5 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Masuda, J. et al., How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex. Structure Fold.Des. (2000)

Release Date

2001-02-07

Peptides

PROPANEDIOL DEHYDRATASE: AD
PROPANEDIOL DEHYDRATASE: BE
PROPANEDIOL DEHYDRATASE: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
L

B
B

E
E

C
G

F
M

PROPANEDIOL DEHYDRATASE

PROPANEDIOL DEHYDRATASE

PROPANEDIOL DEHYDRATASE

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