SMTL ID : 6nab.1

Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: R.150, E.152, F.159, I.160, R.161, S.162, F.165, W.167, Q.235, G.237, T.238, H.240, G.270, L.271, S.272, R.274 Ligands: PRO.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.150, A:E.152, A:E.152, A:S.162, A:Q.235, A:Q.235, A:T.238, A:G.270, A:S.272, A:S.272, A:R.274 Salt bridges: A:R.150 pi-Stacking: A:F.165, A:F.165 pi-Cation interactions: A:R.274, A:R.274 AMP.11: 17 residues within 4Å: Chain B: R.150, E.152, F.159, I.160, R.161, S.162, F.165, W.167, Q.235, G.237, T.238, H.240, G.270, L.271, S.272, R.274 Ligands: PRO.12 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.150, B:E.152, B:E.152, B:S.162, B:Q.235, B:Q.235, B:T.238, B:G.270, B:S.272, B:S.272, B:R.274 Salt bridges: B:R.150 pi-Stacking: B:F.165, B:F.165 pi-Cation interactions: B:R.274

2 x PRO: PROLINE(Non-covalent)

PRO.2: 13 residues within 4Å: Chain A: T.119, E.121, R.150, W.167, E.169, H.171, F.214, T.238, H.240, S.268, W.269, G.270 Ligands: AMP.1 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.167, A:E.169 Hydrogen bonds: A:T.119, A:T.238, A:T.238, A:S.268, P.2 Salt bridges: A:R.150, A:H.240 PRO.12: 13 residues within 4Å: Chain B: T.119, E.121, R.150, W.167, E.169, H.171, F.214, T.238, H.240, S.268, W.269, G.270 Ligands: AMP.11 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.167, B:E.169 Hydrogen bonds: B:T.119, B:T.119, B:T.119, B:T.238, B:S.268, P.12, P.12 Salt bridges: B:R.150, B:H.240

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.4: 5 residues within 4Å: Chain A: R.294, Q.299, K.395, L.398, D.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.294, A:R.294 Water bridges: A:Q.299 EDO.5: 7 residues within 4Å: Chain A: Y.38, Y.39, V.41, S.42, G.43, C.44, Y.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.39, A:G.43, A:C.44 EDO.6: 4 residues within 4Å: Chain A: R.375, E.380, W.382, K.400 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.375, A:K.400 Water bridges: A:E.380 EDO.7: 7 residues within 4Å: Chain A: F.22, S.23, Y.26, V.157, M.281, T.467, Y.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.230, A:Y.513 Water bridges: A:D.464, A:T.467 EDO.8: 6 residues within 4Å: Chain A: K.18, V.282, H.283, G.284, D.285, K.408 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.282, A:K.408 Water bridges: A:K.18, A:H.283 EDO.9: 4 residues within 4Å: Chain A: R.48, P.49 Chain B: W.131, L.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.48 Water bridges: A:E.34, A:E.34 EDO.10: 4 residues within 4Å: Chain A: K.82, W.101 Chain B: K.104, G.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.106 EDO.14: 3 residues within 4Å: Chain B: R.294, K.395, D.399 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.294, B:R.294 Water bridges: B:Q.299 EDO.15: 7 residues within 4Å: Chain B: Y.38, Y.39, V.41, S.42, G.43, C.44, Y.45 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.39, B:G.43, B:C.44 Water bridges: B:Y.45, B:A.156 EDO.16: 4 residues within 4Å: Chain B: R.375, E.380, W.382, K.400 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.375, B:K.400 Water bridges: B:R.375 EDO.17: 6 residues within 4Å: Chain B: F.22, S.23, Y.26, M.281, T.467, Y.513 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.230 Water bridges: B:S.23, B:D.464 EDO.18: 6 residues within 4Å: Chain B: K.18, V.282, H.283, G.284, D.285, K.408 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.18, B:K.408 Water bridges: B:V.282, B:H.283 EDO.19: 4 residues within 4Å: Chain A: W.131, L.140 Chain B: R.48, P.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.48, B:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP). TO BE PUBLISHED

Release Date

2019-01-30

Peptides

Prolyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prolyl-tRNA synthetase

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