SMTL ID : 3iva.1

Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 40 residues within 4Å: Chain A: I.103, V.110, H.111, G.114, I.117, V.118, G.154, L.155, S.156, L.158, I.159, T.160, L.183, G.185, G.186, A.187, V.209, Q.210, N.211, A.212, T.215, T.305, D.445, R.446, E.449, A.488, P.489, G.490, Y.491, P.492, H.497, K.500, A.522, M.523, P.525, G.526, S.528, V.529, S.530 Ligands: SAH.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:I.103, A:I.117, A:V.118, A:L.158, A:L.158, A:L.183, A:A.187, A:V.209, A:T.215, A:T.305, A:D.445, A:Y.491, A:Y.491, A:Y.491, A:V.529 Hydrogen bonds: A:T.160, A:T.160, A:G.186, A:A.212, A:H.497, A:M.523, A:G.526, A:S.530, A:S.530

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 14 residues within 4Å: Chain A: D.298, R.446, E.449, E.480, R.486, P.487, A.488, Y.491, P.492, A.493, C.494, Y.541, Y.542 Ligands: B12.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.480, A:A.488, A:A.493, A:Y.541, A:Y.542, A:Y.542 Water bridges: A:D.298, A:R.486 Salt bridges: A:R.446 pi-Stacking: A:Y.491, A:Y.541, A:Y.541

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 5 residues within 4Å: Chain A: N.376, V.377, H.379, T.502, E.505 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.505 NO3.4: 6 residues within 4Å: Chain A: N.295, Y.296, E.457, L.472, S.473, N.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.296, A:L.472 NO3.5: 5 residues within 4Å: Chain A: E.480, Y.482, G.484, I.485, S.539 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.484, A:G.484 NO3.6: 2 residues within 4Å: Chain A: D.263, D.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koutmos, M. et al., Insights into the reactivation of cobalamin-dependent methionine synthase. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-11-24

Peptides

Methionine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine synthase

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