- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-oligomer
- Ligands
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
PGO.2: 11 residues within 4Å:- Chain A: H.144, E.171, E.222, T.223, Q.297, S.302, D.336, Q.337, S.363, F.375
- Ligands: K.1
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Q.337, A:F.375
- Hydrogen bonds: A:E.171, A:Q.297
PGO.5: 11 residues within 4Å:- Chain D: H.144, E.171, E.222, T.223, Q.297, S.302, D.336, Q.337, S.363, F.375
- Ligands: K.4
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:Q.337, D:F.375
- Hydrogen bonds: D:E.171, D:E.222, D:Q.297, D:D.336
- 2 x B12: COBALAMIN(Non-covalent)
B12.3: 38 residues within 4Å:- Chain A: T.173, V.174, G.175, A.177, S.203, V.204, E.205, E.206, T.223, S.225, Y.227, D.235, L.268, M.269, S.302, C.303, Q.337, M.374, F.375, A.376
- Chain B: L.46, D.79, V.80, S.81, K.102, T.104, L.115, N.117, L.120, S.122, Q.123, A.124, P.125, V.159, R.160, F.163, M.164, A.167
36 PLIP interactions:23 interactions with chain B, 12 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: B:L.46, B:L.115, B:L.115, B:L.120, B:P.125, B:V.159, B:F.163, B:A.167, A:T.173, A:Y.227, A:L.268
- Hydrogen bonds: B:D.79, B:K.102, B:N.117, B:N.117, B:S.122, B:S.122, B:S.122, B:Q.123, B:A.124, A:T.173, A:A.177, A:E.206, A:E.206, A:S.225, A:M.374, A:A.376
- Water bridges: B:D.79, B:Q.100, B:Q.100, B:T.104, B:L.120, A:E.206, A:T.223
- Salt bridges: B:K.102
- Metal complexes: B12.3
B12.6: 37 residues within 4Å:- Chain D: T.173, V.174, G.175, A.177, S.203, V.204, E.205, E.206, T.223, S.225, Y.227, D.235, L.268, M.269, S.302, C.303, Q.337, M.374, F.375, A.376
- Chain E: L.46, D.79, V.80, S.81, K.102, T.104, L.115, N.117, L.120, S.122, Q.123, A.124, V.159, R.160, F.163, M.164, A.167
39 PLIP interactions:25 interactions with chain E, 13 interactions with chain D, 1 Ligand-Ligand interactions- Hydrophobic interactions: E:L.46, E:L.115, E:L.115, E:L.120, E:L.120, E:V.159, E:F.163, E:A.167, D:T.173, D:Y.227, D:L.268, D:F.375
- Hydrogen bonds: E:D.79, E:K.102, E:N.117, E:N.117, E:S.122, E:S.122, E:S.122, E:Q.123, E:A.124, D:T.173, D:T.173, D:A.177, D:E.206, D:S.225, D:M.374, D:A.376
- Water bridges: E:D.79, E:Q.100, E:Q.100, E:L.120, E:L.120, E:H.171, E:H.171, D:E.206, D:T.223
- Salt bridges: E:K.102
- Metal complexes: B12.6
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yamanishi, M. et al., The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Eur.J.Biochem. (2002)
- Release Date
- 2002-10-02
- Peptides
- Glycerol Dehydratase Alpha subunit: AD
Glycerol Dehydratase Beta subunit: BE
Glycerol Dehydratase 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-oligomer
- Ligands
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 2 x B12: COBALAMIN(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yamanishi, M. et al., The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Eur.J.Biochem. (2002)
- Release Date
- 2002-10-02
- Peptides
- Glycerol Dehydratase Alpha subunit: AD
Glycerol Dehydratase Beta subunit: BE
Glycerol Dehydratase Gamma subunit: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
LB
BE
EC
GF
M