SMTL ID : 5ysh.2 (1 other biounit)

Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Q.141, E.170, E.221, Q.296, S.362 Ligands: PGO.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.170, A:E.221, A:S.362 CA.7: 6 residues within 4Å: Chain D: Q.141, E.170, E.221, Q.296, S.362 Ligands: PGO.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.170, D:E.221, D:S.362

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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.261, A:E.265, A:E.280, H2O.2 K.3: 5 residues within 4Å: Chain A: L.203, E.205, E.208, T.222 Ligands: B12.6 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.8: 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:S.264, D:E.280, H2O.12, H2O.14 K.9: 5 residues within 4Å: Chain D: L.203, E.205, E.208, T.222 Ligands: B12.12 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 PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 12 residues within 4Å: Chain A: H.143, E.170, E.221, T.222, Q.296, V.300, S.301, D.335, Q.336, S.362, F.374 Ligands: CA.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.336, A:F.374 Hydrogen bonds: A:E.170, A:Q.296, A:Q.296, A:D.335 PGO.10: 12 residues within 4Å: Chain D: H.143, E.170, E.221, T.222, Q.296, V.300, S.301, D.335, Q.336, S.362, F.374 Ligands: CA.7 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.300, D:Q.336, D:F.374 Hydrogen bonds: D:E.170, D:Q.296, D:Q.296, D:D.335

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

5AD.5: 12 residues within 4Å: Chain A: S.224, V.225, Y.226, T.259, S.260, G.261, S.264, S.299, V.300, S.301, C.302 Ligands: B12.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.261, A:S.264, A:S.301 Water bridges: A:G.261 5AD.11: 11 residues within 4Å: Chain D: S.224, V.225, Y.226, T.259, S.260, G.261, S.264, S.299, V.300, S.301 Ligands: B12.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.299, D:S.301 Water bridges: D:S.264, D:S.264

2 x B12: COBALAMIN(Non-covalent)

B12.6: 33 residues within 4Å: Chain A: A.172, V.173, S.202, 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, Q.173, S.176 Ligands: K.3, 5AD.5 36 PLIP interactions: 24 interactions with chain B, 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.89, B:A.90, B:L.124, B:L.129, B:L.129, B:P.131, B:Y.172, A:Y.226, A:Q.267 Hydrogen bonds: B:D.88, B:K.111, B:N.126, B:N.126, B:P.131, B:P.131, B:Q.132, B:A.133, B:Q.173, B:S.176, B:S.176, A:S.202, A:E.205, A:E.205, A:S.224, A:M.373 Water bridges: B:D.88, B:Q.109, B:Q.109, B:L.129, B:H.180, A:V.173, A:K.242, A:K.242, A:Q.267 Salt bridges: B:K.111 Metal complexes: B12.6 B12.12: 32 residues within 4Å: Chain D: A.172, V.173, S.202, 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, Q.173, S.176 Ligands: K.9, 5AD.11 33 PLIP interactions: 22 interactions with chain E, 10 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:Y.226, D:Q.267 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:Q.173, E:S.176, E:S.176, D:V.173, D:S.202, D:E.205, D:E.205, D:Q.267, D:M.373 Water bridges: E:Q.109, E:Q.109, D:A.174, D:A.176 Salt bridges: E:K.111 Metal complexes: B12.12

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
G

D
J

B
H

E
K

C
I

F
L

Diol dehydrase alpha subunit

Diol dehydrase beta subunit

Diol dehydrase gamma subunit

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