SMTL ID : 6vvh.1

Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) in complex with lysine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 10 residues within 4Å: Chain A: G.67, Q.68, M.70, W.72, H.75, N.99, Y.125 Chain B: N.99, E.103 Ligands: LYS.4 10 PLIP interactions: 3 interactions with chain B, 3 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: B:N.99, B:E.103, K.1, K.4, A:Q.68, A:H.75 Water bridges: B:Y.125, K.4, A:Y.125 Hydrophobic interactions: A:W.72 LYS.4: 10 residues within 4Å: Chain A: N.99, E.103 Chain B: G.67, Q.68, M.70, W.72, H.75, N.99, Y.125 Ligands: LYS.1 9 PLIP interactions: 5 interactions with chain B, 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrophobic interactions: B:W.72 Hydrogen bonds: B:H.75, B:Y.125, K.1, K.1, A:N.99, A:N.99 Water bridges: B:G.97, B:G.97 LYS.6: 10 residues within 4Å: Chain C: G.67, Q.68, M.70, W.72, H.75, N.99, Y.125 Chain D: N.99, E.103 Ligands: LYS.11 9 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: C:W.72 Hydrogen bonds: C:H.75, C:Y.125, D:N.99, D:E.103, K.11, K.11 Water bridges: C:G.97, C:G.97 LYS.11: 10 residues within 4Å: Chain C: N.99, E.103 Chain D: G.67, Q.68, M.70, W.72, H.75, N.99, Y.125 Ligands: LYS.6 10 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C, 3 Ligand-Ligand interactions Hydrophobic interactions: D:W.72 Hydrogen bonds: D:Q.68, D:H.75, C:N.99, C:E.103, K.6, K.6, K.11 Water bridges: D:Y.125, C:Y.125

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

NA.2: 5 residues within 4Å: Chain A: A.27, I.59, G.62, L.120, K.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.178 Water bridges: A:T.63 NA.5: 5 residues within 4Å: Chain B: A.27, I.59, G.62, L.120, K.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.178 Water bridges: B:T.63 NA.7: 5 residues within 4Å: Chain C: A.27, I.59, G.62, L.120, K.178 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.63, C:K.178 Water bridges: C:K.178 NA.12: 5 residues within 4Å: Chain D: A.27, I.59, G.62, L.120, K.178 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.63, D:K.178 Water bridges: D:K.178

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain B: W.72, I.76, E.103, H.106, A.107, Q.110 Chain D: D.73 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:D.73, D:D.73, B:Q.110, B:Q.110 GOL.9: 6 residues within 4Å: Chain B: D.73 Chain D: W.72, I.76, E.103, H.106, Q.110 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.110, D:Q.110, B:D.73 GOL.10: 7 residues within 4Å: Chain B: R.37, F.38, E.74, M.77 Chain D: H.106, E.109, Q.110 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:F.38, D:E.109, D:Q.110, C:R.320

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 3 residues within 4Å: Chain D: P.162, R.185, E.188 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.185, D:R.185 Water bridges: D:K.192 Salt bridges: D:E.188, D:E.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, C.J. et al., Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms. Febs J. (2021)

Release Date

2021-02-24

Peptides

4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic

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