SMTL ID : 7kpc.1 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 10 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Chain B: N.96 Ligands: EDO.11, LYS.18 9 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: A:A.64, A:H.71, B:N.96, B:N.96, K.1 Water bridges: A:G.94, B:S.95, B:Y.122 Salt bridges: K.1 LYS.18: 10 residues within 4Å: Chain A: N.96 Chain B: S.63, A.64, L.66, H.68, H.71, N.96, Y.122 Ligands: LYS.1, EDO.11 7 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:H.71, B:Y.122, A:N.96, A:N.96 Water bridges: B:S.63, B:Y.122 Salt bridges: K.18

7 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.3 MG.3: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: K.33, V.34, E.70 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.70 MG.5: 1 residues within 4Å: Chain A: G.182 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: E.240, N.241, Y.242, K.243 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: P.152, E.158 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

ACT.8: 3 residues within 4Å: Chain A: K.83, G.84, T.85 No protein-ligand interaction detected (PLIP) ACT.9: 6 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, N.264 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:Y.149, A:N.264 Water bridges: A:R.154, A:R.154 Salt bridges: A:R.154 ACT.10: 3 residues within 4Å: Chain A: K.292, E.293, A.296 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.293 Water bridges: A:K.297 ACT.20: 4 residues within 4Å: Chain B: I.19, D.52, H.235, L.238 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.19, B:L.238 Hydrogen bonds: B:I.19 Salt bridges: B:H.235 ACT.21: 5 residues within 4Å: Chain B: A.275, L.277, I.307, K.308, G.309 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.310 ACT.22: 2 residues within 4Å: Chain B: T.98, H.99 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.99

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

EDO.11: 7 residues within 4Å: Chain A: H.68, S.95, A.97, Q.100 Chain B: A.64 Ligands: LYS.1, LYS.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.68, A:S.95, B:A.64 EDO.12: 3 residues within 4Å: Chain A: E.240, N.241 Ligands: MG.6 No protein-ligand interaction detected (PLIP) EDO.13: 3 residues within 4Å: Chain A: L.274, M.302, I.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.302 EDO.14: 5 residues within 4Å: Chain A: F.168, C.171, E.172, I.174, Y.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.171 Water bridges: A:Y.175 EDO.23: 3 residues within 4Å: Chain B: A.232, H.235, F.236 No protein-ligand interaction detected (PLIP) EDO.24: 4 residues within 4Å: Chain A: T.67, R.284 Chain B: H.99 Ligands: EDO.28 No protein-ligand interaction detected (PLIP) EDO.25: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, Y.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254 EDO.26: 4 residues within 4Å: Chain B: E.48, N.49, G.50, K.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.231, B:S.231, B:K.308 EDO.27: 3 residues within 4Å: Chain B: P.152, G.156, C.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.156 EDO.28: 6 residues within 4Å: Chain A: T.65, R.284 Chain B: A.97, H.99, Q.100 Ligands: EDO.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.100 Water bridges: B:H.99 EDO.29: 5 residues within 4Å: Chain A: A.97, H.99, Q.100 Chain B: T.65, R.284 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.100 Water bridges: A:H.99, B:T.65

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

PGE.15: 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.16: 3 residues within 4Å: Chain A: K.303, K.304, K.306 No protein-ligand interaction detected (PLIP) PGE.30: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129 PGE.31: 6 residues within 4Å: Chain B: A.40, R.41, K.44, I.47, E.48, T.81 No protein-ligand interaction detected (PLIP) PGE.32: 5 residues within 4Å: Chain B: K.109, G.112, A.113, D.114, I.144 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.114, B:D.114

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

PEG.17: 4 residues within 4Å: Chain A: G.182, N.183, I.184, D.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.184, A:D.185 Water bridges: A:S.181 PEG.33: 7 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.154, B:G.202, B:N.264

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.34: 4 residues within 4Å: Chain B: G.50, I.51, D.52, H.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.50, B:D.52 Water bridges: B:D.52, B:K.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND. To Be Published

Release Date

2021-11-17

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

4-hydroxy-tetrahydrodipicolinate synthase

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