- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x K: POTASSIUM ION(Non-covalent)
- 4 x NH4: AMMONIUM ION(Non-functional Binders)
NH4.2: 5 residues within 4Å:- Chain A: G.261, S.264, E.265, E.280, C.283
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:G.261, A:E.265
- Water bridges: A:S.264, A:S.264
NH4.3: 5 residues within 4Å:- Chain A: L.203, E.205, E.208, T.222
- Ligands: CNC.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:T.222, A:T.222
NH4.7: 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:S.264, D:E.280
- Water bridges: D:S.264
NH4.8: 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:E.208
- Water bridges: D:E.205
- 2 x PGR: R-1,2-PROPANEDIOL(Non-covalent)
PGR.4: 11 residues within 4Å:- Chain A: H.143, E.170, E.221, T.222, Q.296, S.301, D.335, Q.336, S.362, F.374
- Ligands: K.1
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.374
- Hydrogen bonds: A:E.170, A:Q.296
PGR.9: 11 residues within 4Å:- Chain D: H.143, E.170, E.221, T.222, Q.296, S.301, D.335, Q.336, S.362, F.374
- Ligands: K.6
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:Q.336, D:F.374
- Hydrogen bonds: D:E.170, D:E.221, D:Q.296, D:D.335
- 2 x CNC: CYANOCOBALAMIN(Non-covalent)
CNC.5: 33 residues within 4Å:- Chain A: T.172, A.174, S.202, E.205, T.222, S.224, Y.226, D.234, 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: NH4.3
39 PLIP interactions:25 interactions with chain B, 13 interactions with chain A, 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, 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:Q.197, B:S.200, B:S.200, A:S.202, A:E.205, A:E.205, A:S.224, A:M.373
- Water bridges: B:Q.133, B:Q.133, B:L.153, B:H.204, A:A.176, A:A.176, A:E.205, A:K.242, A:Q.267
- Salt bridges: B:K.135
- Metal complexes: CNC.5
CNC.10: 35 residues within 4Å:- Chain D: T.172, V.173, A.174, A.176, S.202, E.205, T.222, S.224, 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, K.135, T.137, L.148, N.150, L.153, P.155, Q.156, A.157, P.158, N.188, R.193, Y.196, Q.197, S.200
- Ligands: NH4.8
34 PLIP interactions:22 interactions with chain E, 11 interactions with chain D, 1 Ligand-Ligand interactions- Hydrophobic interactions: E:L.148, E:L.148, E:L.153, E:L.153, E:P.155, E:P.158, E:Y.196, D:Q.267
- Hydrogen bonds: E:D.112, E:K.135, E:N.150, E:P.155, E:P.155, E:Q.156, E:A.157, E:Q.197, E:S.200, E:S.200, D:T.172, D:T.172, D:A.176, D:E.205, D:S.224, D:S.224, D:Q.267, D:M.373, D:A.375
- Water bridges: E:D.112, E:Q.133, E:L.153, E:L.153, 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
AD
LB
BE
EC
GF
M
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x K: POTASSIUM ION(Non-covalent)
- 4 x NH4: AMMONIUM ION(Non-functional Binders)
- 2 x PGR: R-1,2-PROPANEDIOL(Non-covalent)
- 2 x CNC: CYANOCOBALAMIN(Non-covalent)
- 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
AD
LB
BE
EC
GF
M