- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FYB: ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide(Non-covalent)
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 6 residues within 4Å:- Chain A: G.35, I.36, N.37, P.40, T.160, L.161
Ligand excluded by PLIPEDO.3: 7 residues within 4Å:- Chain A: L.81, F.84, I.128, E.129, L.132, D.133, L.134
Ligand excluded by PLIPEDO.4: 6 residues within 4Å:- Chain A: R.211, E.221, E.223
- Chain B: L.207, R.211
- Ligands: EDO.23
Ligand excluded by PLIPEDO.5: 6 residues within 4Å:- Chain A: L.227, Q.228, T.229
- Chain B: F.523, P.524
- Ligands: EDO.18
Ligand excluded by PLIPEDO.6: 4 residues within 4Å:- Chain A: I.482, D.483, E.484, E.485
Ligand excluded by PLIPEDO.7: 4 residues within 4Å:- Chain A: M.351, A.396, D.400, E.439
Ligand excluded by PLIPEDO.8: 4 residues within 4Å:- Chain A: Y.213, N.312, Y.316, R.319
Ligand excluded by PLIPEDO.9: 6 residues within 4Å:- Chain A: M.307, E.311, P.345, W.346, R.348, H.412
Ligand excluded by PLIPEDO.12: 8 residues within 4Å:- Chain A: P.457, L.458, R.461, L.487, C.491
- Chain B: Y.15, L.16, Y.21
Ligand excluded by PLIPEDO.14: 4 residues within 4Å:- Chain A: K.74, V.75, R.76, E.141
Ligand excluded by PLIPEDO.16: 6 residues within 4Å:- Chain A: Y.15, H.18, D.20, Y.21, I.167, S.168
Ligand excluded by PLIPEDO.18: 5 residues within 4Å:- Chain A: Q.228, A.259, K.262
- Chain B: F.523
- Ligands: EDO.5
Ligand excluded by PLIPEDO.19: 3 residues within 4Å:- Chain A: R.205, A.320, L.321
Ligand excluded by PLIPEDO.21: 8 residues within 4Å:- Chain A: Y.15, L.16, Y.21
- Chain B: P.457, L.458, R.461, L.487, C.491
Ligand excluded by PLIPEDO.23: 7 residues within 4Å:- Chain A: L.207, R.211, I.274
- Chain B: R.211, E.221, E.223
- Ligands: EDO.4
Ligand excluded by PLIPEDO.24: 5 residues within 4Å:- Chain A: F.523
- Chain B: Q.228, A.259, K.262
- Ligands: EDO.27
Ligand excluded by PLIPEDO.25: 5 residues within 4Å:- Chain B: F.84, I.128, E.129, L.132, L.134
Ligand excluded by PLIPEDO.26: 5 residues within 4Å:- Chain A: Q.492
- Chain B: P.170, D.178, R.182, A.188
Ligand excluded by PLIPEDO.27: 7 residues within 4Å:- Chain A: F.523, P.524
- Chain B: P.225, L.227, Q.228, T.229
- Ligands: EDO.24
Ligand excluded by PLIPEDO.28: 4 residues within 4Å:- Chain B: E.281, G.282, D.284, H.287
Ligand excluded by PLIPEDO.30: 3 residues within 4Å:- Chain B: A.396, D.400, E.439
Ligand excluded by PLIPEDO.31: 6 residues within 4Å:- Chain B: L.418, E.419, T.421, P.422, L.463, Q.467
Ligand excluded by PLIPEDO.33: 4 residues within 4Å:- Chain B: D.195, K.198, T.199, T.512
Ligand excluded by PLIPEDO.34: 4 residues within 4Å:- Chain B: D.284, R.285, S.516, R.518
Ligand excluded by PLIPEDO.37: 4 residues within 4Å:- Chain B: E.376, T.379, S.380, L.381
Ligand excluded by PLIPEDO.39: 6 residues within 4Å:- Chain B: Y.15, H.18, D.20, Y.21, I.167, S.168
Ligand excluded by PLIPEDO.40: 4 residues within 4Å:- Chain A: R.428
- Chain B: P.40, Y.41, Q.42
Ligand excluded by PLIPEDO.41: 6 residues within 4Å:- Chain B: M.307, E.311, P.345, W.346, R.348, H.412
Ligand excluded by PLIPEDO.42: 2 residues within 4Å:- Chain B: D.431, T.433
Ligand excluded by PLIPEDO.43: 3 residues within 4Å:- Chain B: A.66, R.69, E.71
Ligand excluded by PLIP- 7 x SO4: SULFATE ION(Non-functional Binders)
SO4.10: 6 residues within 4Å:- Chain A: Y.358, K.406, L.407, I.408, A.409, H.411
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Y.358, A:I.408, A:A.409
- Salt bridges: A:H.411
SO4.11: 5 residues within 4Å:- Chain A: H.287, C.404, K.445, E.446, R.506
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.446
- Water bridges: A:E.446
- Salt bridges: A:R.506
SO4.15: 8 residues within 4Å:- Chain A: A.234, E.235, T.420, T.421, R.437, N.449, Y.451
- Ligands: PEG.13
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:E.235, A:N.449, A:Y.451
- Water bridges: A:G.233, A:Y.451
- Salt bridges: A:R.437
SO4.17: 3 residues within 4Å:- Chain A: S.218, F.219, L.220
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:F.219
- Water bridges: B:N.98
SO4.29: 5 residues within 4Å:- Chain B: H.287, C.404, K.445, E.446, R.506
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:H.287, B:E.446, B:E.446
- Salt bridges: B:K.445, B:R.506
SO4.32: 3 residues within 4Å:- Chain B: G.175, L.176, A.177
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.176, B:A.177
- Water bridges: B:D.178
SO4.36: 6 residues within 4Å:- Chain B: Y.358, K.406, L.407, I.408, A.409, H.411
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:I.408, B:A.409
- Salt bridges: B:H.411
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.13: 11 residues within 4Å:- Chain A: G.232, G.233, A.234, E.235, I.258, P.422, L.423, L.464, Q.467, D.483
- Ligands: SO4.15
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.233, A:E.235, A:Q.467
- Water bridges: A:Y.231, A:D.483, A:D.483
PEG.38: 8 residues within 4Å:- Chain B: R.285, T.286, Y.330, L.333, L.443, K.445, M.510, A.515
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.285, B:Y.330
- 2 x LYS: LYSINE(Non-covalent)
LYS.20: 16 residues within 4Å:- Chain A: G.233, A.234, S.255, E.257, R.279, M.293, E.295, Y.297, N.449, A.450, Y.451, E.453, G.499, F.500, G.501
- Ligands: FYB.1
8 PLIP interactions:8 interactions with chain A,- Hydrophobic interactions: A:Y.451
- Hydrogen bonds: A:G.233, A:S.255, A:N.449, A:E.453
- Water bridges: A:R.279, A:R.279
- Salt bridges: A:R.279
LYS.44: 17 residues within 4Å:- Chain B: G.233, A.234, S.255, E.257, R.279, M.293, E.295, Y.297, N.449, A.450, Y.451, E.453, G.499, F.500, G.501
- Ligands: FYB.22, PG4.35
12 PLIP interactions:11 interactions with chain B, 1 Ligand-Ligand interactions- Hydrophobic interactions: B:Y.451
- Hydrogen bonds: B:G.233, B:S.255, B:E.257, B:E.295, B:Y.297, B:N.449, B:E.453, K.44
- Water bridges: B:R.279, B:R.279
- Salt bridges: B:R.279
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.35: 14 residues within 4Å:- Chain B: G.232, G.233, A.234, E.235, I.258, T.420, T.421, P.422, R.437, N.449, Y.451, Q.467, D.483
- Ligands: LYS.44
10 PLIP interactions:1 Ligand-Ligand interactions, 9 interactions with chain B- Hydrogen bonds: K.44, B:G.233, B:R.437, B:N.449, B:Y.451, B:Q.467, B:D.483, B:D.483
- Water bridges: B:E.235, B:K.471
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dranow, D.M. et al., Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand. to be published
- Release Date
- 2019-03-27
- Peptides
- Lysine--tRNA ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FYB: ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide(Non-covalent)
- 30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x SO4: SULFATE ION(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x LYS: LYSINE(Non-covalent)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dranow, D.M. et al., Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand. to be published
- Release Date
- 2019-03-27
- Peptides
- Lysine--tRNA ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B