SMTL ID : 7kxh.1 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

2 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.1: 19 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, H.71, N.96, E.100, Y.122 Chain D: S.63, A.64, L.66, T.67, H.68, H.71, N.96, E.100, Y.122 Ligands: MG.3 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:H.71, A:N.96, A:N.96, A:E.100, D:H.71, D:N.96, D:N.96, D:N.96, D:Y.122 Water bridges: A:Y.122 3VN.15: 17 residues within 4Å: Chain B: S.63, A.64, L.66, H.68, H.71, N.96, E.100, Y.122 Chain C: S.63, A.64, L.66, T.67, H.68, H.71, N.96, E.100, Y.122 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:H.71, B:N.96, B:N.96, B:N.96, C:H.71, C:N.96, C:N.96, C:E.100, C:Y.122 Water bridges: B:Y.122

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.2, H2O.4 MG.3: 7 residues within 4Å: Chain A: A.64, T.65, L.66, T.67 Chain D: H.99, E.100 Ligands: 3VN.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.66, H2O.23 MG.7: 1 residues within 4Å: Chain B: D.239 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.239, H2O.9, H2O.10 MG.16: 5 residues within 4Å: Chain C: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain C: E.36 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain D: R.154, N.264 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain D: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain D: K.44 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.8: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166 PGE.18: 6 residues within 4Å: Chain C: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.166 Water bridges: C:S.160, C:D.170 PGE.26: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.166 Water bridges: D:Q.129

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 6 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, N.264 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:Y.149, A:N.264 Salt bridges: A:R.154 ACT.9: 6 residues within 4Å: Chain B: T.59, Y.149, V.151, R.154, K.178, N.264 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.151 Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.10: 2 residues within 4Å: Chain B: I.47, E.48 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.47 Hydrogen bonds: B:E.48 ACT.19: 6 residues within 4Å: Chain C: T.59, Y.149, R.154, K.178, F.260, N.264 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.260 Hydrogen bonds: C:N.264 Salt bridges: C:R.154 ACT.20: 3 residues within 4Å: Chain B: L.285 Chain C: T.98, H.99 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.98, B:L.285 ACT.27: 7 residues within 4Å: Chain D: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.216

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain A: K.303, K.304, Y.305, K.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.304 PEG.30: 2 residues within 4Å: Chain D: P.152, G.156 No protein-ligand interaction detected (PLIP) PEG.31: 3 residues within 4Å: Chain D: K.15, R.169, R.196 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.15

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

EDO.11: 1 residues within 4Å: Chain C: H.99 No protein-ligand interaction detected (PLIP) EDO.12: 7 residues within 4Å: Chain A: Y.208, Y.242, K.246 Chain B: S.212, G.214, E.240, Y.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.240 EDO.13: 1 residues within 4Å: Chain B: F.236 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain B: D.228, M.229, A.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.228 EDO.21: 3 residues within 4Å: Chain C: I.19, M.198, K.216 No protein-ligand interaction detected (PLIP) EDO.22: 8 residues within 4Å: Chain C: D.250, E.251, Y.253, N.254, K.304, Y.305 Chain D: A.192, H.193 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.253, C:N.254, C:N.254, C:K.304, C:Y.305 EDO.28: 3 residues within 4Å: Chain A: T.67, R.284 Chain D: H.99 No protein-ligand interaction detected (PLIP) EDO.29: 3 residues within 4Å: Chain D: G.112, A.113, D.114 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS. To Be Published

Release Date

2021-12-08

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

4-hydroxy-tetrahydrodipicolinate synthase

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