SMTL ID : 4q3a.4 (5 other biounits)

PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

NAI.1: 26 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, 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, 2YC.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.126 Hydrogen bonds: A:A.3, A:Q.123, A:K.152, A:V.153, A:A.173, A:D.174, A:T.205, 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

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

NA.2: 7 residues within 4Å: Chain A: E.203, T.205, C.207, G.226, I.227, 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

1 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: NAI.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.130, A:E.246, A:E.246

1 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:L.5, A:I.61, A:F.64, A:F.64, A:F.109 Hydrogen bonds: A:L.5, A:V.54, A:V.54, A:I.61, A:I.61

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

PYLD, pyrrolysine synthase

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