SMTL ID : 8b1n.1

Crystal structure of TrmD-Tm1570 from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.170, E.171, E.179 Chain B: E.118 Ligands: SAM.15 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.170, A:E.171, A:E.179, B:E.118, H2O.6 MG.12: 5 residues within 4Å: Chain A: E.118 Chain B: E.170, E.171, E.179 Ligands: SAM.5 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.170, B:E.171, B:E.179, A:E.118, H2O.15

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: F.13, P.14, E.15 Chain B: Y.23 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: S.337, L.338 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: S.368, I.369, E.370, R.426 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: Y.23 Chain B: F.13, P.14, E.15 Ligand excluded by PLIP

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 17 residues within 4Å: Chain A: T.358, T.359, A.360, F.384, G.385, G.387, W.388, G.389, P.404, I.405, N.412, H.413, L.414, V.416, A.419, Y.423 Chain B: R.283 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.358, A:A.360, A:G.385, A:I.405, A:I.405, A:L.414 Water bridges: A:F.390, A:H.413 Salt bridges: A:H.413 SAM.5: 25 residues within 4Å: Chain A: L.89, D.90, P.91, G.115, R.116, Y.117, E.118, G.119, I.133, S.134, I.135, G.136, F.138, V.139, I.140, T.141, G.142, G.143, A.146 Chain B: R.156, N.166, E.171, S.172, E.179 Ligands: MG.12 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.172, B:E.179, A:L.89, A:G.115, A:I.135, A:G.136, A:F.138, A:I.140 Salt bridges: B:E.171 SAM.15: 25 residues within 4Å: Chain A: R.156, N.166, E.171, S.172, E.179, H.182 Chain B: L.89, D.90, P.91, G.115, R.116, Y.117, E.118, G.119, I.133, S.134, I.135, G.136, F.138, V.139, I.140, T.141, G.142, G.143 Ligands: MG.1 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.89, B:G.115, B:I.135, B:G.136, B:F.138, B:I.140, A:S.172, A:E.179 Water bridges: B:D.90 Salt bridges: A:E.171 SAM.16: 16 residues within 4Å: Chain B: T.358, T.359, A.360, F.384, G.385, G.387, W.388, G.389, P.404, I.405, N.412, H.413, L.414, V.416, A.419, Y.423 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.358, B:T.358, B:G.385, B:I.405, B:I.405, B:L.414 Water bridges: B:F.390 Salt bridges: B:H.413

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: P.181, T.217, N.221 Chain B: R.92, R.125, M.132 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.213, A:N.221 Water bridges: A:T.217, A:T.217, B:D.122, B:R.125 GOL.7: 9 residues within 4Å: Chain A: I.20, F.21, Y.23, L.26, D.152 Chain B: M.16, R.116, T.141, L.145 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.116, B:R.116, B:T.141, A:I.20, A:Y.23, A:Y.23 Water bridges: B:G.142, A:L.26 GOL.8: 5 residues within 4Å: Chain A: R.286, G.289, V.290, K.291, Y.331 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:C.285 Water bridges: A:R.286, B:D.410 GOL.9: 4 residues within 4Å: Chain A: Y.56, Q.57, Y.58 Chain B: R.185 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.185 GOL.10: 7 residues within 4Å: Chain A: R.92, D.122, R.125, M.132 Chain B: P.181, T.217, N.221 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:D.122, A:D.122, A:R.125, B:T.217, B:Q.220 Hydrogen bonds: B:N.221 GOL.11: 2 residues within 4Å: Chain A: K.192 Chain B: E.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.192 GOL.17: 3 residues within 4Å: Chain B: L.127, A.129, D.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.127 GOL.18: 9 residues within 4Å: Chain A: M.16, R.116, T.141, L.145 Chain B: I.20, F.21, Y.23, L.26, D.152 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.152, A:R.116, A:R.116, A:T.141 Water bridges: A:E.144, A:E.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sulkowska, J., Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. To be published. To Be Published

Release Date

2022-09-28

Peptides

tRNA (guanine-N(1)-)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (guanine-N(1)-)-methyltransferase