SMTL ID : 4q3b.5 (5 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 27 residues within 4Å: Chain A: A.3, N.122, Q.123, T.126, V.148, G.149, 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.3, 2YF.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.126, A:P.225 Hydrogen bonds: A:Q.123, A:Y.130, A:K.152, A:V.153, A:A.173, A:D.174, A:T.205, A:P.225, A:I.227 Water bridges: A:G.151, A:G.154, A:G.251 Salt bridges: A:K.152, A:K.152 NAI.14: 26 residues within 4Å: Chain B: A.3, N.122, Q.123, 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, G.226, I.227, E.246, P.247, L.248 Ligands: MG.16, 2YF.17 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.126, B:P.225 Hydrogen bonds: B:Q.123, B:G.149, 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:T.205, A:C.207 Water bridges: A:A.230 NA.15: 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: 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.16: 7 residues within 4Å: Chain B: Y.130, E.246, L.248, G.249, I.250, G.251 Ligands: NAI.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.246

2 x 2YF: N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine(Non-covalent)

2YF.4: 15 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, L.248 Ligands: NAI.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.5, A:I.61, A:F.64, A:F.64, A:A.104, A:F.109, A:L.248 Hydrogen bonds: 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.105 2YF.17: 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: NAI.14 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.5, B:I.61, B:F.64, B:F.64, B:A.104, 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:F.64

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

EDO.5: 6 residues within 4Å: Chain A: S.135, R.136, Y.137, A.140, S.142, F.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.137 EDO.18: 4 residues within 4Å: Chain B: K.33, K.37, S.44, G.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.37, B:K.37 Water bridges: B:K.33, B:K.33 EDO.19: 4 residues within 4Å: Chain B: F.80, D.83, E.92, N.96 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.83, B:N.96 EDO.20: 5 residues within 4Å: Chain B: K.197, L.216, S.217, E.218, Y.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.197

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: D.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.165 GOL.7: 3 residues within 4Å: Chain A: T.6, P.7, D.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.6, A:D.8 GOL.8: 6 residues within 4Å: Chain A: K.19, A.20, A.23, L.243, I.244, A.245 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.19, A:R.236, A:L.243 Water bridges: A:A.20, A:A.245, A:A.245 GOL.9: 4 residues within 4Å: Chain A: L.39, Y.40, I.128, H.160 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.39, A:K.164 GOL.10: 7 residues within 4Å: Chain A: V.162, F.166, R.167, V.168, G.186, I.187, I.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.168 Water bridges: A:F.166 GOL.11: 1 residues within 4Å: Chain A: F.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.152, A:R.180 GOL.12: 5 residues within 4Å: Chain A: E.132, S.135, R.136, K.164, F.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.132, A:S.135, A:K.164 Water bridges: A:R.136 GOL.13: 2 residues within 4Å: Chain A: Q.18, S.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.18, A:S.22 GOL.21: 3 residues within 4Å: Chain B: T.42, F.43, L.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.43, B:E.47, B:E.47 GOL.22: 4 residues within 4Å: Chain B: K.37, G.41, T.42, F.43 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.37, B:K.37 Water bridges: B:K.37 GOL.23: 8 residues within 4Å: Chain B: L.10, I.11, N.12, I.13, N.63, A.66, S.67 Ligands: PEG.29 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.10, B:I.13 Water bridges: B:N.12, B:N.12, B:N.12, B:N.12, B:N.14 GOL.24: 3 residues within 4Å: Chain B: Q.73, D.78, S.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.73, B:Q.73, B:S.79 GOL.25: 3 residues within 4Å: Chain B: L.39, Y.40, I.128 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.39, B:H.160 GOL.26: 5 residues within 4Å: Chain B: A.20, R.236, L.243, I.244, A.245 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.236, B:R.236, B:A.245 Water bridges: B:A.20

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

PEG.27: 3 residues within 4Å: Chain B: Q.25, E.26, G.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.26 PEG.28: 9 residues within 4Å: Chain A: V.54, S.56, D.86, V.87, Y.90, M.103 Chain B: D.86, V.87, M.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.86 PEG.29: 2 residues within 4Å: Chain B: N.14 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.14

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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