- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 2 x CA: CALCIUM ION(Non-covalent)
CA.2: 6 residues within 4Å:- Chain A: Q.141, E.170, E.221, Q.296, S.362
- Ligands: PGO.1
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:E.170, A:E.221, A:S.362
CA.8: 6 residues within 4Å:- Chain D: Q.141, E.170, E.221, Q.296, S.362
- Ligands: PGO.7
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:E.170, D:E.221, D:S.362
- 2 x K: POTASSIUM ION(Non-covalent)
K.3: 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:E.265, A:E.280, A:C.283, H2O.3, H2O.8
K.9: 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:C.283, H2O.39, H2O.40
- 2 x NH4: AMMONIUM ION(Non-functional Binders)
NH4.4: 6 residues within 4Å:- Chain A: Q.200, S.202, E.208, A.220, E.221, T.222
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.208, A:E.221, A:T.222
NH4.10: 5 residues within 4Å:- Chain D: Q.200, S.202, E.208, E.221, T.222
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:E.208, D:E.221, D:T.222
- 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.5: 13 residues within 4Å:- Chain A: T.222, S.224, V.225, Y.226, T.259, S.260, G.261, S.264, S.299, V.300, S.301, C.302
- Ligands: B12.6
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:T.222, A:S.224, A:G.261, A:S.301
- Water bridges: A:S.224, A:S.264, A:S.264, A:S.301
FWK.11: 13 residues within 4Å:- Chain D: T.222, S.224, V.225, Y.226, T.259, S.260, G.261, S.264, S.299, V.300, S.301, C.302
- Ligands: B12.12
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:T.222, D:G.261, D:S.301
- Water bridges: D:S.224, D:S.264, D:S.264, D:S.301
- 2 x B12: COBALAMIN(Non-covalent)(Covalent)
B12.6: 25 residues within 4Å:- Chain A: E.205, S.224, Y.226, D.234, G.235, Q.267, M.268, C.302
- 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.5
32 PLIP interactions:7 interactions with chain A, 24 interactions with chain B, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:Y.226, A:Q.267, B:V.89, B:A.90, B:L.124, B:L.129, B:L.129, B:P.131, B:P.134, B:Y.172
- Hydrogen bonds: A:S.224, A:D.234, A:G.235, B:K.111, B:N.126, B:N.126, B:P.131, B:P.131, B:Q.132, B:A.133, B:Q.173, B:S.176, B:S.176
- Water bridges: A:K.242, A:Q.267, B:D.88, B:Q.109, B:Q.109, B:N.126, B:H.180
- Salt bridges: B:K.111
- Metal complexes: B12.6
B12.12: 26 residues within 4Å:- Chain D: E.205, S.224, Y.226, D.234, G.235, Q.267, M.268, S.301, C.302
- 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.11
31 PLIP interactions:9 interactions with chain D, 20 interactions with chain E, 1 interactions with chain F, 1 Ligand-Ligand interactions- Hydrophobic interactions: D:Y.226, D:Q.267, E:V.89, E:A.90, E:L.124, E:L.129, E:L.129, E:P.131, E:P.134, E:Y.172
- Hydrogen bonds: D:S.224, D:Y.226, D:D.234, D:G.235, D:Q.267, E:T.113, E:N.126, E:N.126, E:P.131, E:P.131, E:Q.132, E:A.133, E:Q.173, E:S.176
- Water bridges: D:K.242, D:K.242, E:Q.132, E:S.176, F:R.91
- Salt bridges: E:K.111
- Metal complexes: B12.12
- 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
AD
DB
BE
EC
CF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 2 x CA: CALCIUM ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x NH4: AMMONIUM ION(Non-functional Binders)
- 2 x FWK: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol(Non-covalent)
- 2 x B12: COBALAMIN(Non-covalent)(Covalent)
- 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
AD
DB
BE
EC
CF
F