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

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 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: 13 residues within 4Å: Chain A: S.63, A.64, L.66, H.71, N.96, E.100, Y.122 Chain B: S.63, A.64, H.71, N.96, E.100, Y.122 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:H.71, A:N.96, A:N.96, A:E.100, A:Y.122, B:H.71, B:N.96, B:N.96, B:N.96 Water bridges: B:G.94, B:E.100, B:E.100 3VN.20: 13 residues within 4Å: Chain C: S.63, A.64, H.71, N.96, E.100, Y.122 Chain D: S.63, A.64, L.66, H.71, N.96, E.100, Y.122 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:A.64, D:H.71, D:N.96, D:N.96, C:H.71, C:N.96, C:N.96, C:Y.122 Water bridges: D:G.94

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

EDO.2: 6 residues within 4Å: Chain A: A.139, Q.140, D.170, C.171, E.172, N.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.139, A:E.172 EDO.9: 2 residues within 4Å: Chain A: S.291 Chain B: Q.129 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:K.292, B:Q.129, B:Q.129 EDO.10: 6 residues within 4Å: Chain B: G.202, E.203, D.204, A.205, N.256, F.260 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.202, B:D.204, B:A.205 Water bridges: B:E.203 EDO.11: 4 residues within 4Å: Chain B: G.20, D.52, H.235, L.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.235 Water bridges: B:I.19 EDO.12: 3 residues within 4Å: Chain B: D.189 Chain D: Y.253, K.257 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Water bridges: B:T.161, B:T.161, B:D.189, B:D.189 Hydrogen bonds: D:Y.253 EDO.16: 4 residues within 4Å: Chain C: F.236, E.244, K.247, I.248 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.244, C:E.244 EDO.17: 3 residues within 4Å: Chain C: S.12, M.13, D.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.12, C:D.14 EDO.21: 2 residues within 4Å: Chain D: K.292, E.293 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.292, D:K.292 EDO.22: 4 residues within 4Å: Chain D: I.258, K.297, E.300, V.301 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.301

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

PGE.3: 8 residues within 4Å: Chain A: L.281, E.282, F.283, L.285, L.287, C.288, S.289 Chain B: E.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.283, A:S.289, A:S.289, A:S.289 PGE.13: 6 residues within 4Å: Chain B: V.79, C.82, K.83, V.89, G.112, D.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.114 PGE.14: 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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.163, C:K.166 Water bridges: C:Y.132, C:S.160 PGE.23: 7 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 Ligands: ACT.29 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: C.82, T.85, V.87, K.88, D.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.82, A:K.88, A:K.88 Water bridges: A:K.83, A:G.84, A:G.112 GOL.19: 5 residues within 4Å: Chain C: K.83, T.85, V.87, K.88, D.114 2 PLIP interactions: 2 interactions with chain C Water bridges: C:C.82, C:D.114

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

PEG.5: 4 residues within 4Å: Chain A: Q.129, Y.132, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:Y.132 PEG.6: 8 residues within 4Å: Chain A: L.191, P.195, R.196, M.197, G.214, K.216 Chain C: K.246, D.250 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.196, C:K.246, C:D.250 Water bridges: C:D.250 PEG.24: 3 residues within 4Å: Chain D: S.291, E.293, N.294 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.291, D:E.293, D:E.293 Water bridges: D:N.294, D:N.294, C:Q.128 PEG.25: 3 residues within 4Å: Chain D: V.79, K.83, G.112 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.83, D:G.112

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

ACT.7: 6 residues within 4Å: Chain A: N.16, D.143, I.144, P.145, E.172, N.173 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.173 Hydrogen bonds: A:N.16, A:N.16 ACT.8: 7 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, L.238, E.240, Y.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.242 Salt bridges: A:K.216 ACT.15: 4 residues within 4Å: Chain B: A.68, H.71, R.72, L.104 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.68, B:L.104 Hydrogen bonds: B:A.68 Salt bridges: B:R.72 ACT.26: 6 residues within 4Å: Chain C: P.152, G.153, G.156 Chain D: P.152, G.153, G.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.156 ACT.27: 2 residues within 4Å: Chain C: H.99 Chain D: T.67 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.284, C:H.99 ACT.28: 7 residues within 4Å: Chain D: Y.149, V.151, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:K.125, D:R.154 Hydrogen bonds: D:N.264 ACT.29: 5 residues within 4Å: Chain D: Q.128, S.160, D.162, T.163 Ligands: PGE.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.160, D:D.162, D:T.163 Water bridges: D:D.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS. To Be Published

Release Date

2021-12-01

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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