- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
NA.2: 6 residues within 4Å:- Chain A: E.203, T.205, C.207, G.226, I.227, P.228
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.203, A:C.207
- Water bridges: A:T.224
NA.23: 6 residues within 4Å:- Chain B: E.203, T.205, C.207, G.226, P.228, A.230
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.205, B:C.207
- Water bridges: B:A.230
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 7 residues within 4Å:- Chain A: Y.130, E.246, L.248, G.249, I.250, G.251
- Ligands: NAI.1
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:Y.130, A:E.246
MG.24: 8 residues within 4Å:- Chain B: Y.130, E.246, P.247, L.248, G.249, I.250, G.251
- Ligands: NAI.22
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:Y.130, B:E.246, B:E.246
- 2 x 2YC: N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine(Non-covalent)
2YC.4: 14 residues within 4Å:- Chain A: L.4, L.5, P.53, V.54, G.59, I.60, I.61, F.64, A.104, D.105, F.109, N.122, P.247
- Ligands: NAI.1
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:L.5, A:I.61, A:F.64, A:F.109
- Hydrogen bonds: A:L.5, A:V.54, A:V.54, A:I.61, A:A.104
- Water bridges: A:S.65, A:D.105
2YC.25: 14 residues within 4Å:- Chain B: L.4, L.5, P.53, V.54, G.59, I.60, I.61, F.64, A.104, D.105, F.109, N.122, P.247
- Ligands: NAI.22
15 PLIP interactions:15 interactions with chain B- Hydrophobic interactions: B:L.5, B:L.5, B:I.61, B:F.64, B:F.64, B:F.109
- Hydrogen bonds: B:L.5, B:V.54, B:V.54, B:I.61, B:A.104
- Water bridges: B:A.3, B:F.64, B:S.65, B:D.105
- 13 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 3 residues within 4Å:- Chain A: Q.25, G.29, L.30
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.25
- Water bridges: A:D.31
GOL.6: 3 residues within 4Å:- Chain A: T.42, F.43, L.260
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:F.43, A:F.43, A:E.47
GOL.7: 5 residues within 4Å:- Chain A: G.62, N.63, F.64, S.65, A.66
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:N.63, A:S.65, A:S.65, A:A.66
- Water bridges: A:I.61, A:F.64
GOL.8: 4 residues within 4Å:- Chain A: Q.73, D.78, S.79
- Ligands: SO4.11
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.73, A:Q.73, A:S.79
GOL.9: 7 residues within 4Å:- Chain A: L.10, I.11, N.12, I.13, N.63, A.66, S.67
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.12, A:I.13
- Water bridges: A:N.12
GOL.10: 5 residues within 4Å:- Chain A: K.19, A.20, L.243, I.244, A.245
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.245
- Water bridges: A:A.20, A:A.23
GOL.26: 4 residues within 4Å:- Chain B: E.159, Q.163, N.184, L.185
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.159, B:Q.163, B:L.185
GOL.27: 6 residues within 4Å:- Chain A: D.86, V.87, M.103
- Chain B: V.54, D.86, V.87
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.86, B:D.86
GOL.28: 7 residues within 4Å:- Chain B: A.38, L.39, E.132, R.136, H.160, K.164
- Ligands: EDO.36
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.38, B:E.132, B:R.136
GOL.29: 7 residues within 4Å:- Chain B: K.19, A.20, A.23, R.236, L.243, I.244, A.245
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.236, B:A.245
GOL.30: 7 residues within 4Å:- Chain B: L.10, I.11, N.12, I.13, N.63, A.66, S.67
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.12, B:I.13, B:A.66
- Water bridges: B:N.12
GOL.31: 4 residues within 4Å:- Chain B: S.46, Q.73, G.76, F.77
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.73, B:G.76
GOL.32: 3 residues within 4Å:- Chain B: Q.73, D.78, S.79
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Q.73, B:Q.73, B:D.78, B:D.78, B:S.79
- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.11: 5 residues within 4Å:- Chain A: S.46, Q.73, G.76, F.77
- Ligands: GOL.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.46, A:Q.73, A:Q.73
SO4.12: 5 residues within 4Å:- Chain A: A.38, L.39, E.132, R.136, K.164
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:E.132
- Water bridges: A:R.136, A:K.164, A:K.164
- Salt bridges: A:R.136, A:K.164
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.13: 6 residues within 4Å:- Chain A: Y.40, M.119, A.120, C.125, I.128, S.258
2 PLIP interactions:2 interactions with chain A- Water bridges: A:M.119, A:M.119
PEG.14: 7 residues within 4Å:- Chain A: L.114, K.115, N.116, G.117
- Chain B: L.114, K.115, N.116
No protein-ligand interaction detected (PLIP)PEG.33: 5 residues within 4Å:- Chain B: K.118, M.119, A.120, C.125, S.258
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:M.119, B:S.258
- Water bridges: B:N.121, B:N.121
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.15: 4 residues within 4Å:- Chain A: F.166, R.167, V.168, G.186
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:V.168
EDO.16: 2 residues within 4Å:- Chain A: K.48, F.80
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.48, A:K.48
EDO.17: 3 residues within 4Å:- Chain A: P.53, I.60, D.83
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.65
EDO.18: 1 residues within 4Å:- Chain A: Q.18
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.22
EDO.19: 6 residues within 4Å:- Chain A: L.150, G.151, K.152, F.155, L.177, R.180
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.150, A:R.180
EDO.20: 5 residues within 4Å:- Chain A: S.45, S.46, E.47, E.99, K.115
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.115
- Water bridges: A:S.46
EDO.21: 1 residues within 4Å:- Chain A: L.39
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.39
- Water bridges: A:Q.163
EDO.34: 5 residues within 4Å:- Chain B: V.162, F.166, R.167, V.168, G.186
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:V.168, B:V.168
EDO.35: 4 residues within 4Å:- Chain B: S.135, R.136, K.164, F.166
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.164
EDO.36: 3 residues within 4Å:- Chain B: L.39, I.128
- Ligands: GOL.28
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.39
- Water bridges: B:Q.163, B:Q.163
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Quitterer, F. et al., The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD). Angew.Chem.Int.Ed.Engl. (2014)
- Release Date
- 2014-04-23
- Peptides
- PYLD, pyrrolysine synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x 2YC: N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine(Non-covalent)
- 13 x GOL: GLYCEROL(Non-functional Binders)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Quitterer, F. et al., The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD). Angew.Chem.Int.Ed.Engl. (2014)
- Release Date
- 2014-04-23
- Peptides
- PYLD, pyrrolysine synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
A