SMTL ID : 9cbr.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x C2F: 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID(Non-covalent)

C2F.1: 15 residues within 4Å: Chain A: E.373, N.376, G.379, S.380, K.381, D.443, N.464, V.490, D.531, G.570, S.572, N.573, F.576, R.583, I.603 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.373 Hydrogen bonds: A:G.379, A:K.381, A:D.443, A:N.464, A:N.464, A:G.570, A:R.583, A:R.583 Water bridges: A:E.373, A:R.374, A:N.376, A:D.531, A:L.532 Salt bridges: A:D.443, A:D.531, A:R.583

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.256, C.322, C.323 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.256, A:C.322, A:C.323 ZN.4: 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)

B12.3: 39 residues within 4Å: Chain A: G.57, T.58, Q.61, G.77, P.79, Y.120, P.154, G.155, T.156, T.192, Q.194, E.226, L.232, A.257, G.285, L.286, Y.296, C.323, V.760, H.761, I.763, G.764, L.767, 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 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:T.58, A:P.79, A:T.192, A:L.286, A:I.763, A:L.767, A:V.768, A:L.808, A:L.809, A:V.810, A:I.833, A:A.857 Hydrogen bonds: A:Q.61, A:Q.61, A:Y.120, A:Y.120, A:Q.194, A:E.226, A:A.257, A:Y.296, A:Y.296, A:V.810, A:G.836, A:A.860 Water bridges: A:M.56, A:G.285, A:D.762, A:I.763, A:I.763, A:G.764, A:A.837, A:A.837

1 x K: POTASSIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Menjdoza, J. et al., Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (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