- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 4 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:E.265, A:E.280, H2O.4, H2O.7
K.3: 5 residues within 4Å:- Chain A: L.203, E.205, E.208, T.222
- Ligands: B12.8
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:L.203, A:E.205, A:E.208, A:T.222, A:T.222
K.11: 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.33, H2O.34
K.12: 5 residues within 4Å:- Chain D: L.203, E.205, E.208, T.222
- Ligands: B12.16
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:L.203, D:E.205, D:E.208, D:T.222, D:T.222
- 1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)
5AD.5: 14 residues within 4Å:- Chain A: T.222, S.224, V.225, T.259, S.260, G.261, S.264, S.299, V.300, S.301, C.302, F.374
- Ligands: PGO.4, B12.8
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:F.374
- Hydrogen bonds: A:S.224, A:G.261, A:S.264, A:S.301
- Water bridges: A:G.261
5AD.13: 14 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, F.374
- Ligands: B12.16
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:F.374
- Hydrogen bonds: D:S.224, D:S.264, D:S.299, D:S.301
- Water bridges: D:G.261, D:G.261, D:Q.296
- 6 x CL: CHLORIDE ION(Non-functional Binders)
CL.6: 3 residues within 4Å:- Chain A: K.21, E.22, P.310
Ligand excluded by PLIPCL.7: 3 residues within 4Å:- Chain A: R.532
- Chain D: M.120, N.121
Ligand excluded by PLIPCL.9: 3 residues within 4Å:- Chain A: K.288
- Chain C: D.63, R.64
Ligand excluded by PLIPCL.14: 3 residues within 4Å:- Chain D: K.21, E.22, P.310
Ligand excluded by PLIPCL.15: 3 residues within 4Å:- Chain A: M.120, N.121
- Chain D: R.532
Ligand excluded by PLIPCL.17: 5 residues within 4Å:- Chain D: K.288
- Chain F: G.61, R.62, D.63, R.64
Ligand excluded by PLIP- 2 x B12: COBALAMIN(Non-covalent)
B12.8: 36 residues within 4Å:- Chain A: T.172, V.173, A.174, A.176, S.202, L.203, E.204, E.205, T.222, S.224, Y.226, D.234, Q.267, M.268, S.301, Q.336, M.373, F.374, A.375
- 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, S.176
- Ligands: K.3, 5AD.5
42 PLIP interactions:27 interactions with chain B, 14 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: B:V.89, B:A.90, B:L.124, B:L.124, B:L.129, B:L.129, B:P.131, B:Y.172, A:T.172, A:V.173, A:Y.226, A:Q.267
- Hydrogen bonds: B:D.88, B:D.88, B:K.111, B:T.113, B:N.126, B:P.131, B:P.131, B:Q.132, B:A.133, B:S.176, B:S.176, A:T.172, A:V.173, A:E.205, A:E.205, A:M.373, A:A.375
- Water bridges: B:D.88, B:D.88, B:Q.109, B:Q.109, B:L.129, B:L.129, B:Q.173, A:Y.226, A:K.242, A:Q.267, A:Q.267
- Salt bridges: B:K.111
- Metal complexes: B12.8
B12.16: 36 residues within 4Å:- Chain D: T.172, V.173, A.174, A.176, S.202, L.203, E.204, E.205, T.222, S.224, Y.226, D.234, Q.267, M.268, S.301, Q.336, M.373, F.374, A.375
- 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, S.176
- Ligands: K.12, 5AD.13
43 PLIP interactions:14 interactions with chain D, 28 interactions with chain E, 1 Ligand-Ligand interactions- Hydrophobic interactions: D:T.172, D:V.173, D:Y.226, D:Q.267, D:A.375, E:V.89, E:A.90, E:L.124, E:L.124, E:L.129, E:L.129, E:P.131, E:P.134, E:Y.172
- Hydrogen bonds: D:T.172, D:T.172, D:V.173, D:E.205, D:M.373, D:A.375, E:D.88, E:K.111, E:N.126, E:P.131, E:P.131, E:Q.132, E:A.133, E:S.176, E:S.176
- Water bridges: D:K.242, D:K.242, D:Q.267, E:D.88, E:D.88, E:Q.109, E:Q.109, E:Q.109, E:L.129, E:L.129, E:Q.173, E:H.180
- Salt bridges: E:K.111
- Metal complexes: B12.16
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shibata, N. et al., Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis. Angew. Chem. Int. Ed. Engl. (2018)
- Release Date
- 2018-09-19
- 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
GD
JB
HE
KC
IF
L
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 4 x K: POTASSIUM ION(Non-covalent)
- 1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)
- 6 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x B12: COBALAMIN(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shibata, N. et al., Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis. Angew. Chem. Int. Ed. Engl. (2018)
- Release Date
- 2018-09-19
- 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
GD
JB
HE
KC
IF
L