SMTL ID : 5yrt.1 (1 other biounit)

Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: Q.141, E.170, E.221, Q.296, S.362 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.170, A:E.221, A:S.362, H2O.2, H2O.6 CA.9: 5 residues within 4Å: Chain D: Q.141, E.170, E.221, Q.296, S.362 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.170, D:E.221, D:S.362, H2O.29, H2O.34

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.2, H2O.3 K.3: 5 residues within 4Å: Chain A: L.203, E.205, E.208, T.222 Ligands: B12.7 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.10: 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.30, H2O.35 K.11: 6 residues within 4Å: Chain D: L.203, E.205, E.208, T.222, I.223 Ligands: B12.15 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

2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.4: 14 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, F.374 Ligands: B12.7 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.12: 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: B12.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.374 Hydrogen bonds: D:S.224, D:S.224, D:G.261, D:S.264, D:S.301 Water bridges: D:G.261, D:Q.296

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: K.21, E.22, P.310 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.532 Chain D: M.120, N.121 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: K.288 Chain C: R.62, D.63, R.64 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain D: K.21, E.22, P.310 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: M.120, N.121 Chain D: R.532 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: K.288 Chain F: R.62, D.63, R.64 Ligand excluded by PLIP

2 x B12: COBALAMIN(Non-covalent)

B12.7: 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.4 38 PLIP interactions: 13 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.124, B:L.129, B:L.129, B:P.131, B:Y.172 Hydrogen bonds: A:T.172, A:T.172, A:V.173, A:E.205, A:E.205, A:M.373, A:A.375, B:D.88, B:D.88, B:K.111, B:N.126, B:P.131, B:P.131, B:Q.132, B:A.133, B:S.176, B:S.176 Water bridges: A:K.242, A:K.242, A:Q.267, A:Q.267, B:Q.109, B:Q.109, B:L.129, B:L.129, B:Q.173 Salt bridges: B:K.111 Metal complexes: B12.7 B12.15: 35 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, 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.11, 5AD.12 39 PLIP interactions: 25 interactions with chain E, 13 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: E:V.89, E:L.124, E:L.124, E:L.129, E:L.129, E:P.131, E:P.134, E:Y.172, D:T.172, D:Y.226, D:Q.267, D:A.375 Hydrogen bonds: E:D.88, 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, D:T.172, D:T.172, D:V.173, D:E.205, D:M.373, D:A.375 Water bridges: E:D.88, E:Q.109, E:Q.109, E:L.129, E:L.129, E:Q.173, D:Y.226, D:Q.267, D:Q.267 Salt bridges: E:K.111 Metal complexes: B12.15

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
A

D
D

B
B

E
E

C
C

F
F

Diol dehydrase alpha subunit

Diol dehydrase beta subunit

Diol dehydrase gamma subunit

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