SMTL ID : 9cbp.1

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Pre-Catalytic State (Pre-Hcy-on)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: I.537, R.545, L.626, D.629, R.631, P.637, L.638 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.537, A:R.545, A:R.545, A:D.629 GOL.2: 11 residues within 4Å: Chain A: L.152, G.153, P.154, Y.173, L.190, E.191, A.193, D.195, Q.198, V.199, A.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.152, A:E.191, A:D.195, A:Q.198 Water bridges: A:Q.194 GOL.5: 8 residues within 4Å: Chain A: L.370, Q.402, E.405, A.407, V.604, D.605, A.606, P.721 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.405, A:E.405, A:V.604, A:A.606 Water bridges: A:E.373 GOL.6: 8 residues within 4Å: Chain A: P.351, L.362, E.526, L.529, G.564, V.565, G.566, T.600 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.600 Water bridges: A:G.566 GOL.7: 5 residues within 4Å: Chain A: W.166, Y.170, E.451, K.455, H.485 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.167 GOL.8: 6 residues within 4Å: Chain A: S.165, W.166, D.167, K.455, Y.456 Ligands: GOL.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.166, A:D.167, A:D.167, A:K.455, A:Y.456, A:Y.456 GOL.9: 9 residues within 4Å: Chain A: L.25, V.26, R.27, G.29, S.246, G.522, L.523, R.524, D.527 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.27, A:G.29, A:S.246, A:R.524 Water bridges: A:R.460 GOL.10: 10 residues within 4Å: Chain A: V.159, S.160, G.162, W.166, L.197, P.430, A.433, K.455, Y.456 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.160, A:G.162, A:W.166 Water bridges: A:S.160 GOL.11: 8 residues within 4Å: Chain A: T.445, S.465, A.466, N.467, D.470, R.474, F.475, V.478 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.445, A:N.467, A:N.467, A:D.470, A:D.470, A:R.474

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

HCS.3: 10 residues within 4Å: Chain A: A.55, M.56, G.57, E.106, E.191, T.192, C.256, C.322, C.323 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.56, A:G.57, A:E.191

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.256, C.322, C.323 Ligands: HCS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.256, A:C.322, A:C.323 ZN.13: 4 residues within 4Å: Chain A: C.7, C.11, H.13, H.520 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.11, A:H.13, A:H.520

1 x B12: COBALAMIN(Non-covalent)

B12.12: 37 residues within 4Å: Chain A: Q.364, E.365, A.366, S.367, H.408, L.703, M.706, F.713, L.720, V.723, L.724, A.727, K.731, L.753, G.758, D.759, V.760, H.761, D.762, I.763, G.764, V.768, G.804, M.805, S.806, L.808, L.809, V.810, I.833, G.835, G.836, A.837, A.857, E.858, D.859, A.860, G.863 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:E.365, A:L.703, A:F.713, A:L.720, A:V.723, A:A.727, A:L.753, A:V.760, A:V.768, A:L.809, A:I.833, A:A.857 Hydrogen bonds: A:E.365, A:E.365, A:H.408, A:K.731, A:V.760, A:H.761, A:D.762, A:D.762, A:D.762, A:I.763, A:G.764, A:V.810, A:G.836, A:A.837, A:A.860 Metal complexes: A:H.761

1 x K: POTASSIUM ION(Non-covalent)

K.14: 5 residues within 4Å: Chain A: D.53, G.54, E.106, L.281, G.321 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.53, A:D.53, A:G.54, A:G.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mendoza, J. et al., Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Pre-Catalytic State (Pre-Hcy-on). To Be Published

Release Date

2025-06-25

Peptides

Methionine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine synthase