SMTL ID : 7k9m.1

Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x W5Y: 5'-O-(L-phenylalanylsulfamoyl)adenosine(Non-covalent)

W5Y.1: 24 residues within 4Å: Chain A: H.175, S.177, Q.180, R.201, D.203, T.208, H.209, T.210, F.213, Q.215, E.217, F.255, F.257, T.258, E.279, W.280, G.281, G.282, C.283, A.305, F.306, G.307, G.309, R.312 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.258, A:A.305 Hydrogen bonds: A:H.175, A:S.177, A:S.177, A:R.201, A:D.203, A:T.210, A:Q.215, A:E.279, A:G.309, A:R.312 Water bridges: A:Q.158, A:T.176 Salt bridges: A:R.201 pi-Stacking: A:F.213, A:F.213, A:F.255, A:F.257 W5Y.14: 24 residues within 4Å: Chain D: H.175, S.177, Q.180, R.201, D.203, T.208, H.209, T.210, F.213, Q.215, E.217, F.255, F.257, T.258, E.279, W.280, G.281, G.282, C.283, A.305, F.306, G.307, G.309, R.312 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:T.258, D:A.305 Hydrogen bonds: D:S.177, D:S.177, D:R.201, D:D.203, D:D.203, D:T.210, D:Q.215, D:E.279, D:G.309, D:R.312 Water bridges: D:Q.158, D:T.176 Salt bridges: D:R.201 pi-Stacking: D:F.213, D:F.213, D:F.255, D:F.257

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: R.251, H.253, E.263 Chain B: E.40 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.263, A:E.263, B:E.40 MG.3: 2 residues within 4Å: Chain A: G.156, Q.158 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.156, A:Q.158, H2O.2, H2O.3, H2O.4 MG.8: 5 residues within 4Å: Chain A: E.259 Chain B: D.176, D.471, D.477, E.480 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:E.259, B:E.480, H2O.7, H2O.7, H2O.7, H2O.8 MG.15: 4 residues within 4Å: Chain D: R.251, H.253, E.263 Chain E: E.40 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:E.263, D:E.263, E:E.40 MG.16: 2 residues within 4Å: Chain D: G.156, Q.158 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.156, D:Q.158, H2O.14, H2O.15, H2O.16 MG.21: 5 residues within 4Å: Chain D: E.259 Chain E: D.176, D.471, D.477, E.480 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: D:E.259, E:E.480, H2O.19, H2O.19, H2O.20, H2O.21

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: A.131, E.132, R.182, T.183, R.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.132, A:R.182, A:R.187, A:R.187 GOL.5: 5 residues within 4Å: Chain A: V.266, W.267, F.268, A.269, F.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.269, A:F.316 GOL.6: 8 residues within 4Å: Chain A: R.249, R.251, D.265, W.277, E.279 Chain B: L.35, E.40, V.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.251, A:D.265, A:E.279 GOL.7: 5 residues within 4Å: Chain A: F.141, R.182, A.186 Chain B: I.620, D.624 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.182, A:R.182, B:D.624 GOL.11: 9 residues within 4Å: Chain A: P.105 Chain B: G.522, D.587, V.588, A.589, A.639, L.641, R.642, V.654 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.639, B:R.642, B:R.642 Water bridges: B:G.522, A:P.105 GOL.12: 6 residues within 4Å: Chain B: P.653, V.654, E.655, Q.704, K.717, G.718 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.655, B:Q.704, B:K.717 Water bridges: B:R.688 GOL.13: 8 residues within 4Å: Chain B: P.277, H.279, A.326, G.329, G.332, E.348, W.352, A.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.329, B:G.332 GOL.17: 5 residues within 4Å: Chain D: A.131, E.132, R.182, T.183, R.187 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.132, D:R.182, D:R.187, D:R.187 GOL.18: 5 residues within 4Å: Chain D: V.266, W.267, F.268, A.269, F.316 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.269, D:F.316 GOL.19: 8 residues within 4Å: Chain D: R.249, R.251, D.265, W.277, E.279 Chain E: L.35, E.40, V.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.251, D:D.265 GOL.20: 5 residues within 4Å: Chain D: F.141, R.182, A.186 Chain E: I.620, D.624 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.182, D:R.182, E:D.624 GOL.24: 9 residues within 4Å: Chain D: P.105 Chain E: G.522, D.587, V.588, A.589, A.639, L.641, R.642, V.654 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:A.639, E:R.642, E:R.642 Water bridges: E:G.522, D:P.105 GOL.25: 6 residues within 4Å: Chain E: P.653, V.654, E.655, Q.704, K.717, G.718 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.655, E:Q.704, E:K.717 Water bridges: E:R.688 GOL.26: 8 residues within 4Å: Chain E: P.277, H.279, A.326, G.329, G.332, E.348, W.352, A.370 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.329, E:G.332

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.9: 7 residues within 4Å: Chain A: G.224, S.302 Chain B: R.432, I.433, G.435, V.436, A.437 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.432, A:S.302 Water bridges: B:G.435 P6G.22: 7 residues within 4Å: Chain D: G.224, S.302 Chain E: R.432, I.433, G.435, V.436, A.437 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.432, D:S.302 Water bridges: E:G.435

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 8 residues within 4Å: Chain B: Q.761, A.764, R.768, D.777, I.778, A.779, L.780 Chain D: P.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.761, B:R.768, B:D.777 Water bridges: B:I.778 PGE.23: 8 residues within 4Å: Chain A: P.100 Chain E: Q.761, A.764, R.768, D.777, I.778, A.779, L.780 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.761, E:R.768, E:D.777 Water bridges: E:I.778

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalska, K. et al., Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation. Nucleic Acids Res. (2021)

Release Date

2021-05-12

Peptides

Phenylalanine--tRNA ligase alpha subunit: AD
Phenylalanine--tRNA ligase beta subunit: BE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit

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