SMTL ID : 4cs4.1

Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: R.144, E.146, H.152, L.153, E.154, F.156, M.158, E.210, L.211, S.212, S.213, G.235, F.236, G.237, E.239, R.240, I.251 Ligands: EDO.9, EDO.21, MG.22, MG.23, AXZ.24 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.144, A:H.152, A:L.153, A:L.153, A:E.210, A:E.210, A:L.211, A:G.237, A:R.240, A:R.240 Water bridges: A:Q.101, A:E.146, A:S.213 Salt bridges: A:R.144 pi-Stacking: A:F.156, A:F.156 pi-Cation interactions: A:R.240, A:R.240 ANP.26: 22 residues within 4Å: Chain B: R.144, E.146, H.152, L.153, E.154, F.156, M.158, E.210, L.211, S.212, S.213, G.235, F.236, G.237, E.239, R.240, I.251 Ligands: EDO.34, EDO.46, MG.47, MG.48, AXZ.49 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.144, B:E.146, B:H.152, B:L.153, B:L.153, B:E.210, B:L.211, B:G.237, B:R.240, B:R.240 Water bridges: B:Q.101, B:E.146, B:S.213 Salt bridges: B:R.144 pi-Stacking: B:F.156, B:F.156 pi-Cation interactions: B:R.240, B:R.240

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

EDO.2: 9 residues within 4Å: Chain A: L.57, G.58, E.61, G.140, P.141, T.157, L.238, R.256 Chain B: K.77 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: Y.56, K.59, L.60, E.63, L.242, K.245, H.246 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: A.116, L.119, A.120, L.123, C.162, I.227, W.231 Ligands: EDO.5, EDO.6 Ligand excluded by PLIP EDO.5: 11 residues within 4Å: Chain A: M.90, A.116, A.120, F.198, I.219, L.221, D.222, W.225, I.227, W.231 Ligands: EDO.4 Ligand excluded by PLIP EDO.6: 12 residues within 4Å: Chain A: A.116, L.119, N.160, F.161, C.162, F.198, V.215, W.231, G.233, A.234 Ligands: EDO.4, EDO.9 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: L.84, I.87, E.88, I.92, D.93, N.94, T.96, S.99, I.102 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: M.196, V.197, F.198, G.199, I.219, P.220, L.221 Ligand excluded by PLIP EDO.9: 11 residues within 4Å: Chain A: M.114, L.115, A.116, R.144, M.158, N.160, F.198, G.235 Ligands: ANP.1, EDO.6, AXZ.24 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: R.170, D.200, T.201, L.202, A.214, V.215, V.216 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: E.54, K.59, R.62, E.63 Chain B: R.66 Ligands: EDO.15 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: K.150, H.206, L.209, K.243, V.244, D.247, F.248, K.249 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: G.72, F.73, K.135 Chain B: Y.49, A.50, R.53 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: G.165, S.166, G.167, C.168, T.169, P.230 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: E.52, K.59 Ligands: EDO.11 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: R.11, V.14, S.259, Y.260, S.265, T.266, N.267 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: L.153, E.154, E.155, K.252, A.255 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: S.35, L.38, S.39, K.42, H.270 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: R.71, F.73, K.135, Q.163, N.172, I.176 Ligand excluded by PLIP EDO.20: 13 residues within 4Å: Chain A: N.55, Y.56, L.57, L.242, F.248, R.253, A.254, A.255, Y.260, Y.261, N.262, G.263 Chain B: K.77 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: E.151, H.152, M.205, D.208, L.209, E.210, R.240 Ligands: ANP.1 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain A: K.77 Chain B: L.57, G.58, E.61, G.140, P.141, T.157, L.238, R.256 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: Y.56, K.59, L.60, E.63, L.242, K.245, H.246 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain B: A.116, L.119, A.120, L.123, C.162, I.227, W.231 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP EDO.30: 11 residues within 4Å: Chain B: M.90, A.116, A.120, F.198, I.219, L.221, D.222, W.225, I.227, W.231 Ligands: EDO.29 Ligand excluded by PLIP EDO.31: 12 residues within 4Å: Chain B: A.116, L.119, N.160, F.161, C.162, F.198, V.215, W.231, G.233, A.234 Ligands: EDO.29, EDO.34 Ligand excluded by PLIP EDO.32: 9 residues within 4Å: Chain B: L.84, I.87, E.88, I.92, D.93, N.94, T.96, S.99, I.102 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: M.196, V.197, F.198, G.199, I.219, P.220, L.221 Ligand excluded by PLIP EDO.34: 11 residues within 4Å: Chain B: M.114, L.115, A.116, R.144, M.158, N.160, F.198, G.235 Ligands: ANP.26, EDO.31, AXZ.49 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: R.170, D.200, T.201, L.202, A.214, V.215, V.216 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: R.66 Chain B: E.54, K.59, R.62, E.63 Ligands: EDO.40 Ligand excluded by PLIP EDO.37: 8 residues within 4Å: Chain B: K.150, H.206, L.209, K.243, V.244, D.247, F.248, K.249 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain A: Y.49, A.50, R.53 Chain B: G.72, F.73, K.135 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain B: G.165, S.166, G.167, C.168, T.169, P.230 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain B: E.52, K.59 Ligands: EDO.36 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain B: R.11, V.14, S.259, Y.260, S.265, T.266, N.267 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: L.153, E.154, E.155, K.252, A.255 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: S.35, L.38, S.39, K.42, H.270 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain B: R.71, F.73, K.135, Q.163, N.172, I.176 Ligand excluded by PLIP EDO.45: 13 residues within 4Å: Chain A: K.77 Chain B: N.55, Y.56, L.57, L.242, F.248, R.253, A.254, A.255, Y.260, Y.261, N.262, G.263 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain B: E.151, H.152, M.205, D.208, L.209, E.210, R.240 Ligands: ANP.26 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.22: 3 residues within 4Å: Chain A: E.210, S.213 Ligands: ANP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.210, A:S.213, H2O.4, H2O.5 MG.23: 4 residues within 4Å: Chain A: Q.101, R.144, H.152 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain B: E.210, S.213 Ligands: ANP.26 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.210, B:S.213, H2O.9, H2O.9 MG.48: 4 residues within 4Å: Chain B: Q.101, R.144, H.152 Ligands: ANP.26 No protein-ligand interaction detected (PLIP)

2 x AXZ: 2-{[DIHYDROXY(4-AMINOETHYLPHENYL)-{4}-SULFANYL]AMINO}-3-HYDROXYPROPANOIC ACID(Non-covalent)

AXZ.24: 15 residues within 4Å: Chain A: I.87, I.92, L.98, S.99, Q.101, I.102, P.113, M.114, R.144, C.195, M.196, V.197, F.198 Ligands: ANP.1, EDO.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.92, A:L.98, A:Q.101, A:I.102, A:P.113, A:P.113 Hydrogen bonds: A:R.144, A:M.196, A:V.197 Water bridges: A:R.144 AXZ.49: 15 residues within 4Å: Chain B: I.87, I.92, L.98, S.99, Q.101, I.102, P.113, M.114, R.144, C.195, M.196, V.197, F.198 Ligands: ANP.26, EDO.34 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.92, B:L.98, B:Q.101, B:I.102, B:P.113, B:P.113 Hydrogen bonds: B:R.144, B:M.196, B:V.197 Water bridges: B:R.144

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.25: 5 residues within 4Å: Chain A: R.124, K.125, R.128 Chain B: N.267, H.269 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.121, A:K.125 Salt bridges: A:R.124, A:K.125, A:R.128 PO4.50: 5 residues within 4Å: Chain A: N.267, H.269 Chain B: R.124, K.125, R.128 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.121, B:K.125 Salt bridges: B:R.124, B:K.125, B:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, M.J. et al., Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells. Chembiochem (2014)

Release Date

2014-04-30

Peptides

PYRROLYSYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRROLYSYL-TRNA SYNTHETASE

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