SMTL ID : 7bbu.2 (1 other biounit)

Crystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x PRO: PROLINE(Non-covalent)

PRO.1: 13 residues within 4Å: Chain A: T.124, E.126, R.155, W.172, E.174, H.176, F.219, T.243, H.245, S.275, W.276, G.277 Ligands: MU5.2 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.172, A:E.174 Hydrogen bonds: A:T.124, A:T.124, A:T.124, A:S.275, P.1, P.1 Water bridges: A:R.155, A:R.155 Salt bridges: A:R.155, A:H.245 PRO.16: 13 residues within 4Å: Chain B: T.124, E.126, R.155, W.172, E.174, H.176, F.219, T.243, H.245, S.275, W.276, G.277 Ligands: MU5.17 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.172, B:E.174 Hydrogen bonds: B:T.124, B:T.124, B:S.275, P.16, P.16 Water bridges: B:R.155, B:R.155 Salt bridges: B:R.155, B:H.245

2 x MU5: ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide(Non-covalent)

MU5.2: 16 residues within 4Å: Chain A: R.155, E.157, K.159, H.160, F.164, L.165, R.166, T.167, F.170, W.172, Q.240, T.243, G.277, T.279, R.281 Ligands: PRO.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.155, A:E.157, A:E.157, A:K.159, A:R.166, A:W.172, A:T.243, A:T.279 Hydrogen bonds: A:T.167, A:T.167, A:T.279, A:R.281 Water bridges: A:E.157 pi-Stacking: A:F.170 MU5.17: 16 residues within 4Å: Chain B: R.155, E.157, K.159, H.160, F.164, L.165, R.166, T.167, F.170, W.172, Q.240, T.243, G.277, T.279, R.281 Ligands: PRO.16 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.155, B:E.157, B:E.157, B:K.159, B:R.166, B:W.172, B:T.243, B:T.279 Hydrogen bonds: B:T.167, B:T.167, B:R.281 pi-Stacking: B:F.170

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

EDO.3: 9 residues within 4Å: Chain A: Y.57, E.61, K.64 Chain B: K.64, N.78, W.150 Ligands: CL.15, EDO.18, CL.30 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.345, A.346, D.347, R.349, W.361 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: F.231, I.232, S.233, V.289, A.419, D.422 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: N.351, Y.352, S.353, W.356 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: L.190, R.212, Y.224, T.226, F.486 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.54, W.55, C.304, R.345 Chain B: E.77 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: R.386, E.391, D.410 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: Y.57, W.60, W.150, C.151, L.171, W.172 Chain B: W.150 Ligands: CL.15, CL.30 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: E.93 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: Y.50, L.52, F.164, T.167, E.169, F.170, L.171, T.280 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain A: K.64, N.78, W.150 Chain B: Y.57, E.61, K.64 Ligands: EDO.3, CL.15, CL.30 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: R.345, A.346, D.347, R.349, W.361 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: F.231, I.232, S.233, V.289, A.419, D.422 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: N.351, Y.352, S.353, W.356 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: L.190, R.212, Y.224, T.226, F.486 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: E.77 Chain B: P.54, W.55, C.304, R.345 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: R.386, E.391, D.410 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain A: W.150 Chain B: Y.57, W.60, W.150, C.151, L.171, W.172 Ligands: CL.15, CL.30 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain B: E.93 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: Y.50, L.52, F.164, T.167, E.169, F.170, L.171, T.280 Ligand excluded by PLIP

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 2 residues within 4Å: Chain A: M.182, A.186 No protein-ligand interaction detected (PLIP) NO3.22: 2 residues within 4Å: Chain B: M.182, A.186 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain A: C.451, C.456, C.498, C.500 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.451, A:C.456, A:C.498, A:C.500 ZN.24: 4 residues within 4Å: Chain B: C.451, C.456, C.498, C.500 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.451, B:C.456, B:C.498, B:C.500

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

CL.15: 5 residues within 4Å: Ligands: EDO.3, EDO.12, EDO.18, EDO.27, CL.30 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Ligands: EDO.3, EDO.12, CL.15, EDO.18, EDO.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Crystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline. To Be Published

Release Date

2022-01-12

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bifunctional glutamate/proline--tRNA ligase

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