SMTL ID : 6vvi.1

Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.68, N.99, Y.125 Chain B: N.99, Y.125 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.99, B:Y.125, A:N.99, A:N.99 Water bridges: B:S.98, B:N.99 GOL.5: 4 residues within 4Å: Chain C: N.99, Y.125 Chain D: N.99, Y.125 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.99, C:N.99, C:Y.125, C:Y.125, D:N.99 GOL.9: 6 residues within 4Å: Chain B: R.37, F.38, E.74 Chain D: H.106, E.109, Q.110 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:F.38, D:E.109, D:E.109, D:Q.110 Water bridges: C:R.320 GOL.10: 7 residues within 4Å: Chain B: D.73 Chain D: W.72, I.76, E.103, H.106, A.107, Q.110 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.72, D:Q.110

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

NA.2: 4 residues within 4Å: Chain A: A.27, I.59, L.120, K.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.178 Water bridges: A:G.62, A:T.63 NA.3: 5 residues within 4Å: Chain B: A.27, I.59, G.62, L.120, K.178 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.63, B:T.64, B:T.64, B:T.64 NA.6: 4 residues within 4Å: Chain C: A.27, I.59, L.120, K.178 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.178 Water bridges: C:K.178 NA.11: 4 residues within 4Å: Chain D: A.27, I.59, L.120, K.178 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.178 Water bridges: D:K.178

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain B: T.63, T.64, Y.150, V.152, R.155, N.256 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.64, B:Y.150, B:N.256 Water bridges: B:T.64 Salt bridges: B:R.155 SO4.7: 3 residues within 4Å: Chain C: R.236, N.237, S.238 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.238, C:S.238 SO4.8: 2 residues within 4Å: Chain C: R.23, F.233 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.23 SO4.12: 3 residues within 4Å: Chain D: R.298, D.306, V.307 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.307 Water bridges: D:R.298 Salt bridges: D:K.294 SO4.13: 3 residues within 4Å: Chain D: I.318, G.319, R.320 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.319, D:R.320

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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