- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 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: GOL.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: GOL.7
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:E.170, D:E.221, D:S.362
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 4 residues within 4Å:- Chain A: K.414, R.417, F.482, D.484
3 PLIP interactions:3 interactions with chain A- Water bridges: A:D.484
- Salt bridges: A:K.414, A:R.417
PO4.5: 3 residues within 4Å:- Chain B: R.174, P.181, Q.182
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Q.182
- Water bridges: B:R.174
- Salt bridges: B:R.174
PO4.6: 3 residues within 4Å:- Chain C: T.75, A.76, Q.77
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: C:T.75, C:T.75, C:Q.77
- Water bridges: C:A.76, A:N.469, A:N.469
PO4.9: 3 residues within 4Å:- Chain D: K.414, R.417, F.482
3 PLIP interactions:3 interactions with chain D- Water bridges: D:K.414
- Salt bridges: D:K.414, D:R.417
PO4.11: 3 residues within 4Å:- Chain E: R.174, P.181, Q.182
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:Q.182
- Water bridges: E:R.174, E:R.174
- Salt bridges: E:R.174
PO4.12: 3 residues within 4Å:- Chain F: T.75, A.76, Q.77
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain F- Water bridges: D:N.469, F:A.76
- Hydrogen bonds: F:Q.77
- 2 x B12: COBALAMIN(Non-covalent)
B12.4: 35 residues within 4Å:- Chain A: T.172, V.173, A.174, A.176, S.202, L.203, 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
47 PLIP interactions:28 interactions with chain B, 18 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: B:V.113, B:A.114, B:L.148, B:L.148, B:L.153, B:L.153, B:P.155, B:P.158, B:Y.196, A:T.172, A:Y.226, A:Q.267, A:F.374
- Hydrogen bonds: B:D.112, B:K.135, B:T.137, 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:T.172, A:V.173, A:A.176, A:E.205, A:E.205, A:S.224, A:S.224, 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:L.153, A:E.205, A:T.222, A:Y.226, A:Q.267, A:Q.267
- Salt bridges: B:K.135
- Metal complexes: B12.4
B12.10: 36 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
43 PLIP interactions:26 interactions with chain E, 16 interactions with chain D, 1 Ligand-Ligand interactions- Hydrophobic interactions: 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:T.172, D:Y.226, 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:V.173, D:A.176, D:E.205, D:S.224, D:S.224, D:M.373, D:A.375
- Water bridges: E:D.112, E:D.112, E:Q.133, E:Q.133, E:Q.133, E:L.153, E:L.153, D:E.205, D:T.222, D:Q.267, D:Q.267
- Salt bridges: E:K.135
- Metal complexes: B12.10
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yamanishi, M. et al., Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols. Febs J. (2012)
- Release Date
- 2012-02-22
- 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 2.10 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x CA: CALCIUM ION(Non-covalent)
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x B12: COBALAMIN(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yamanishi, M. et al., Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols. Febs J. (2012)
- Release Date
- 2012-02-22
- 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