SMTL ID : 4dpq.1

The structure of dihydrodipicolinate synthase 2 from Arabidopsis thaliana in complex with (S)-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: R.337, F.340, V.341, G.342 Ligands: NA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.337, A:F.340 Water bridges: A:G.342 NA.2: 2 residues within 4Å: Chain A: E.338 Ligands: NA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.338 NA.3: 3 residues within 4Å: Chain A: R.247, W.248, G.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.247, A:W.248 NA.5: 5 residues within 4Å: Chain B: R.337, F.340, V.341, G.342 Ligands: NA.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.337 Water bridges: B:G.342, B:E.343 NA.6: 2 residues within 4Å: Chain B: E.338 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.339, B:G.342, B:E.343 NA.8: 5 residues within 4Å: Chain C: R.337, F.340, V.341, G.342 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.337, C:F.340 Water bridges: C:G.342 NA.9: 2 residues within 4Å: Chain C: E.338 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.338 NA.10: 3 residues within 4Å: Chain C: R.247, W.248, G.251 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.247, C:W.248 NA.12: 5 residues within 4Å: Chain D: R.337, F.340, V.341, G.342 Ligands: NA.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.337, D:G.342 Water bridges: D:G.342 NA.13: 2 residues within 4Å: Chain D: E.338 Ligands: NA.12 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.338, D:H.339

4 x LYS: LYSINE(Non-covalent)

LYS.4: 10 residues within 4Å: Chain A: G.106, Q.107, M.109, W.111, H.114, N.138, Y.164 Chain B: N.138, E.142 Ligands: LYS.7 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.138, B:E.142, A:H.114, K.7, K.7 Water bridges: B:Y.164, A:Y.164 Hydrophobic interactions: A:W.111 LYS.7: 10 residues within 4Å: Chain A: N.138, E.142 Chain B: G.106, Q.107, M.109, W.111, H.114, N.138, Y.164 Ligands: LYS.4 9 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: B:W.111 Hydrogen bonds: B:Q.107, B:H.114, B:Y.164, A:N.138, A:E.142, K.4, K.4, K.7 LYS.11: 10 residues within 4Å: Chain C: G.106, Q.107, M.109, W.111, H.114, N.138, Y.164 Chain D: N.138, E.142 Ligands: LYS.14 9 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.138, D:E.142, C:H.114, C:Y.164, K.14, K.14 Hydrophobic interactions: C:W.111 Water bridges: C:G.136, C:G.136 LYS.14: 10 residues within 4Å: Chain C: N.138, E.142 Chain D: G.106, Q.107, M.109, W.111, H.114, N.138, Y.164 Ligands: LYS.11 11 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: C:N.138, C:E.142, D:Q.107, D:H.114, K.11, K.11, K.14 Water bridges: C:Y.164, D:G.136, D:Y.164 Hydrophobic interactions: D:W.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Griffin, M.D.W. et al., Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana. Plos One (2012)

Release Date

2012-07-18

Peptides

Dihydrodipicolinate synthase 2, chloroplastic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydrodipicolinate synthase 2, chloroplastic

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