SMTL ID : 3g5r.1

Crystal structure of Thermus thermophilus TrmFO in complex with tetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 30 residues within 4Å: Chain A: V.7, G.8, A.9, G.10, L.11, A.12, E.31, M.32, R.33, T.38, H.41, V.50, C.51, S.52, E.119, E.120, V.121, A.132, T.133, G.134, P.135, T.137, S.138, L.141, G.335, V.336, G.342, Y.343, S.346 Ligands: THG.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.50, A:P.135 Hydrogen bonds: A:L.11, A:A.12, A:M.32, A:R.33, A:R.33, A:S.52, A:V.121, A:V.121, A:S.138, A:V.336, A:G.342, A:Y.343, A:Y.343, A:S.346 Water bridges: A:G.10, A:G.13, A:H.41, A:S.52, A:S.54, A:L.337, A:L.344 Salt bridges: A:H.41 pi-Stacking: A:Y.343

1 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.2: 6 residues within 4Å: Chain A: P.135, H.308, R.309, N.310, E.341 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.308, A:N.310, A:N.310 Water bridges: A:R.309, A:R.309, A:E.341, A:E.341 pi-Stacking: A:H.308

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: L.84 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:L.84, H2O.3, H2O.4, H2O.12, H2O.12

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: H.152, F.153, Y.312, N.314, G.389, F.390 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.152, A:N.314, A:F.390 Water bridges: A:F.390, A:F.390, A:Q.391 EDO.5: 6 residues within 4Å: Chain A: W.283, I.301, V.302, Y.304, Y.394, N.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.394 Water bridges: A:I.301 EDO.6: 4 residues within 4Å: Chain A: K.360, G.363, L.364, P.365 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: E.324, F.325, R.326, E.329 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.324 EDO.8: 3 residues within 4Å: Chain A: K.35, R.36, M.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.37 EDO.9: 7 residues within 4Å: Chain A: Q.264, E.265, D.266, K.267, T.384, A.385, N.386 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.264, A:T.384 Water bridges: A:N.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimasu, H. et al., Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-05-19

Peptides

Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO

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