SMTL ID : 4q3c.5 (5 other biounits)

PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 24 residues within 4Å: Chain A: A.3, N.122, T.126, V.148, G.149, G.151, K.152, V.153, Y.171, D.172, A.173, D.174, A.204, T.205, P.206, C.207, T.210, P.225, I.227, E.246, P.247, L.248 Ligands: MG.3, 2YG.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.126, A:V.153, A:P.225 Hydrogen bonds: A:A.3, A:Q.123, A:G.151, A:K.152, A:V.153, A:A.173, A:D.174, A:T.205, A:I.227, A:E.246 Water bridges: A:K.152, A:G.154, A:G.251 Salt bridges: A:K.152, A:K.152 NAD.11: 26 residues within 4Å: Chain B: A.3, N.122, Q.123, T.126, V.148, G.151, K.152, V.153, Y.171, D.172, A.173, D.174, L.177, A.204, T.205, P.206, C.207, T.210, P.225, G.226, I.227, E.246, P.247, L.248 Ligands: MG.13, 2YG.14 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.126, B:P.225 Hydrogen bonds: B:A.3, B:Q.123, B:K.152, B:V.153, B:A.173, B:D.174, B:T.205, B:P.225, B:I.227 Water bridges: B:T.126, B:G.151, B:G.154, B:T.210 Salt bridges: B:K.152, B:K.152

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: E.203, T.205, C.207, G.226, P.228, A.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.203, A:C.207 Water bridges: A:A.230 NA.12: 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:E.203, B:C.207 Water bridges: B:T.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 8 residues within 4Å: Chain A: Y.130, E.246, P.247, L.248, G.249, I.250, G.251 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.130, A:E.246 MG.13: 7 residues within 4Å: Chain B: Y.130, E.246, L.248, G.249, I.250, G.251 Ligands: NAD.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.130, B:E.246

2 x 2YG: N~6~-L-lysyl-L-lysine(Non-covalent)

2YG.4: 15 residues within 4Å: Chain A: A.3, 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: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.61, A:F.64, A:F.109 Hydrogen bonds: A:A.3, A:L.5, A:V.54, A:V.54, A:I.61, A:I.61 Water bridges: A:F.64, A:S.65, A:D.106 2YG.14: 15 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, L.248 Ligands: NAD.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.61, B:F.64, B:F.109, B:L.248 Hydrogen bonds: B:L.5, B:V.54, B:V.54, B:I.61, B:I.61 Water bridges: B:S.65, B:D.105, B:N.122, B:Q.123, B:Q.123

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: K.19, A.20, A.23, L.243, I.244, A.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.245 GOL.6: 4 residues within 4Å: Chain A: L.39, Y.40, I.128, H.160 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.40, A:Y.40, A:Q.163 GOL.7: 5 residues within 4Å: Chain A: V.162, F.166, R.167, V.168, G.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.168 Water bridges: A:L.185, A:G.186 GOL.15: 4 residues within 4Å: Chain B: Q.73, F.77, D.78, S.79 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.73, B:D.78, B:S.79, B:S.79

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

EDO.8: 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:I.13, A:A.66 Water bridges: A:N.12 EDO.9: 5 residues within 4Å: Chain A: E.132, S.135, R.136, K.164, F.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.135 Water bridges: A:R.136 EDO.10: 3 residues within 4Å: Chain A: T.28, R.136, L.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.28, A:R.136

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 7 residues within 4Å: Chain A: S.56, D.86, Y.90, M.103 Chain B: S.56, D.86, M.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.56

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
A

B
B

PylD, pyrrolysine synthase

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