SMTL ID : 2i2x.1 (3 other biounits)

Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.164, C.220, C.269, E.313 Ligands: K.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.164, A:E.164, A:C.220, A:C.269 ZN.2: 4 residues within 4Å: Chain A: H.318, E.320 Chain C: H.318, E.320 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.318, C:E.320, A:H.318, A:E.320 ZN.5: 5 residues within 4Å: Chain C: E.164, C.220, C.269, E.313 Ligands: K.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.164, C:C.220, C:C.269

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: E.86, E.164, K.267, E.313 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.86, A:E.164 K.6: 4 residues within 4Å: Chain C: E.86, E.164, E.313 Ligands: ZN.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.86, C:E.164, H2O.15

2 x B13: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE(Non-covalent)

B13.4: 30 residues within 4Å: Chain A: K.169, D.173, A.221, T.225, F.228, A.294, S.314 Chain B: G.133, D.134, V.135, H.136, D.137, I.138, G.139, V.143, T.179, G.180, T.181, L.183, M.184, T.185, A.208, G.210, G.211, G.212, G.228, E.229, E.230, A.231 Chain C: F.321 28 PLIP interactions: 20 interactions with chain B, 8 interactions with chain A, Hydrophobic interactions: B:V.135, B:I.138, A:K.169, A:A.221, A:T.225, A:F.228 Hydrogen bonds: B:G.133, B:D.134, B:V.135, B:H.136, B:D.137, B:D.137, B:D.137, B:I.138, B:G.139, B:T.185, B:T.185, B:A.208, B:G.211, B:G.212, B:E.230, B:A.231, A:A.294, A:S.314 Water bridges: B:T.185, A:D.128, A:D.128 Metal complexes: B:H.136 B13.7: 31 residues within 4Å: Chain A: F.321 Chain C: K.169, D.173, A.221, T.225, F.228, A.294, S.314 Chain D: G.133, D.134, V.135, H.136, D.137, I.138, G.139, V.143, T.179, G.180, T.181, L.183, M.184, T.185, A.208, C.209, G.210, G.211, G.212, G.228, E.229, E.230, A.231 27 PLIP interactions: 7 interactions with chain C, 19 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: C:K.169, C:A.221, C:F.228, D:V.135, D:I.138, D:I.138, D:M.184, A:F.321 Hydrogen bonds: C:A.294, C:S.314, D:G.133, D:V.135, D:D.137, D:D.137, D:I.138, D:G.139, D:T.185, D:T.185, D:A.208, D:G.211, D:G.211, D:G.212, D:E.230, D:A.231 Water bridges: C:D.128, C:D.128 Metal complexes: D:H.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hagemeier, C.H. et al., Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-11-21

Peptides

Methyltransferase 1: AC
Methyltransferase 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Methyltransferase 1

Methyltransferase 1

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