SMTL ID : 4qqu.1

Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

monomer

Ligands

1 x HCS: 2-AMINO-4-MERCAPTO-BUTYRIC ACID(Non-covalent)

HCS.1: 14 residues within 4Å: Chain A: I.468, G.469, S.470, E.521, M.527, M.588, D.636, H.679, C.681, C.761, G.762, K.764 Ligands: ZN.2, 39S.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.468, A:S.470, A:S.470, A:D.636

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.679, C.681, C.761 Ligands: HCS.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.679, A:C.681, A:C.761

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: R.121, Y.549, R.552, H.729, T.765, R.766 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.549, A:Y.549, A:H.729 Salt bridges: A:R.121, A:R.552, A:H.729, A:R.766 PO4.4: 7 residues within 4Å: Chain A: P.687, N.688, K.691, E.713, E.716, Y.717, P.718 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.687, A:E.716 Salt bridges: A:K.691

1 x 39S: N-[4-({[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-gamma-glutamyl-L-glutamic acid(Non-covalent)

39S.5: 22 residues within 4Å: Chain A: R.38, K.41, N.148, H.150, Q.473, K.475, R.478, R.481, N.482, N.525, D.526, M.527, W.545, S.548, Y.549, R.552, Y.553, V.554, W.598, K.764, T.765 Ligands: HCS.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.545, A:R.552, A:V.554 Hydrogen bonds: A:R.38, A:R.38, A:K.143, A:N.148, A:N.148, A:Q.473, A:Q.473, A:S.548, A:S.548, A:Y.553, A:Y.553, A:Y.553 Water bridges: A:R.481, A:D.526, A:Q.529, A:R.555, A:K.764, A:K.764 Salt bridges: A:R.38, A:K.41, A:K.475, A:R.478, A:R.481, A:D.526, A:R.552

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ubhi, D.K. et al., The cobalamin-independent methionine synthase enzyme captured in a substrate-induced closed conformation. J.Mol.Biol. (2015)

Release Date

2015-01-14

Peptides

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

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