SMTL ID : 7xrk.1

Diol dehydratase complexed with AdoMeCbl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.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.2, H2O.3 CA.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.10, H2O.11

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: G.261, S.264, E.265, E.280, C.283 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.261, A:S.264, A:C.283, H2O.1, H2O.3 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:E.265, D:E.280, H2O.10, H2O.10

2 x FWK: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol(Non-covalent)

FWK.3: 12 residues within 4Å: Chain A: T.222, S.224, Y.226, T.259, S.260, G.261, S.264, S.299, V.300, S.301, C.302 Ligands: B12.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.222, A:S.224, A:Y.226, A:Y.226, A:G.261, A:S.264, A:S.301 Water bridges: A:G.261 FWK.7: 12 residues within 4Å: Chain D: T.222, S.224, Y.226, T.259, S.260, G.261, S.264, S.299, V.300, S.301, C.302 Ligands: B12.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.222, D:S.224, D:G.261, D:S.301 Water bridges: D:S.264, D:S.264

2 x B12: COBALAMIN(Non-covalent)

B12.4: 25 residues within 4Å: Chain A: E.205, S.224, Y.226, D.234, G.235, Q.267, M.268, S.301 Chain B: D.88, V.89, A.90, K.111, T.113, L.124, N.126, L.129, P.131, Q.132, A.133, P.134, R.169, Y.172, Q.173, S.176 Ligands: FWK.3 29 PLIP interactions: 22 interactions with chain B, 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.89, B:A.90, B:L.124, B:L.129, B:L.129, B:P.131, B:Y.172 Hydrogen bonds: B:K.111, B:T.113, B:N.126, B:N.126, B:P.131, B:P.131, B:Q.132, B:A.133, B:Q.173, B:S.176, A:S.224, A:Y.226, A:D.234, A:G.235 Water bridges: B:D.88, B:D.88, B:Q.109, B:N.126, A:T.172, A:D.237 Salt bridges: B:K.111 Metal complexes: B12.4 B12.8: 24 residues within 4Å: Chain D: S.224, Y.226, D.234, G.235, Q.267, M.268, S.301 Chain E: D.88, V.89, A.90, K.111, T.113, L.124, N.126, L.129, P.131, Q.132, A.133, P.134, R.169, Y.172, Q.173, S.176 Ligands: FWK.7 26 PLIP interactions: 20 interactions with chain E, 5 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: E:V.89, E:A.90, E:L.124, E:L.129, E:L.129, E:P.131, E:Y.172 Hydrogen bonds: E:K.111, E:N.126, E:N.126, E:P.131, E:P.131, E:Q.132, E:A.133, E:Q.173, E:S.176, D:E.205, D:S.224, D:D.234, D:Q.267, D:Q.267 Water bridges: E:D.88, E:Q.109, E:H.180 Salt bridges: E:K.111 Metal complexes: B12.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, N. et al., Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Chemistry (2022)

Release Date

2023-03-29

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
D

B
B

E
E

C
C

F
F

Diol dehydrase alpha subunit

Diol dehydrase beta subunit

Diol dehydrase gamma subunit

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