SMTL ID : 4q3b.6 (5 other biounits)

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

Coordinates

PDB Format Compare

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, 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, EDO.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.126, A:V.153, A:P.225 Hydrogen bonds: A:Q.123, A:K.152, A:V.153, A:A.173, A:D.174, A:T.205, A:P.225, A:I.227 Water bridges: A:T.126, A:G.151, A:G.154 Salt bridges: A:K.152, A:K.152 NAI.7: 26 residues within 4Å: Chain B: A.3, N.122, 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.9, 2YF.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.126, B:V.153, B:P.225 Hydrogen bonds: B:K.152, B:V.153, B:G.154, B:A.173, B:D.174, B:T.205, B:T.205, B:I.227, B:E.246 Water bridges: B:G.151, B:G.251 Salt bridges: B:K.152

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

NA.2: 7 residues within 4Å: Chain A: E.203, T.205, C.207, G.226, P.228, C.229, A.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.203, A:C.207 Water bridges: A:T.224 NA.8: 7 residues within 4Å: Chain B: E.203, T.205, C.207, G.226, I.227, P.228, A.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.203, 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.130, A:E.246, A:E.246 MG.9: 8 residues within 4Å: Chain B: Y.130, E.246, P.247, L.248, G.249, I.250, G.251 Ligands: NAI.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.130, B:E.246, B:E.246

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

2YF.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, N.122, L.248 Ligands: NAI.1, EDO.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.5, A:I.61, A:F.64, A:A.104, A:L.248 Hydrogen bonds: A:L.5, A:V.54, A:V.54, A:I.61, A:A.104 Water bridges: A:D.105 2YF.10: 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.7 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:A.104 Water bridges: B:D.105

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

EDO.5: 6 residues within 4Å: Chain A: A.3, D.106, R.107, Q.123 Ligands: NAI.1, 2YF.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.107, A:Q.123 EDO.6: 2 residues within 4Å: Chain A: E.99, L.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.114

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: D.86, V.87, M.103 Chain B: V.54, D.86, V.87, Y.90, M.103 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.86, B:D.86

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
C

B
D

PYLD, pyrrolysine synthase

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