SMTL ID : 5ckv.1

DAHP synthase from Mycobacterium tuberculosis, fully inhibited by tyrosine, phenylalanine, and tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-tetramer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: R.145, D.150, A.151 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: P.27, L.28, R.33 Ligands: TYR.17 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: R.145, D.150, A.151 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain D: P.27, L.28, R.33 Ligands: TYR.36 Ligand excluded by PLIP

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

SO4.2: 5 residues within 4Å: Chain A: R.145, S.146, A.147, R.294, K.390 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.146, A:A.147 Salt bridges: A:R.145, A:R.294, A:K.390 SO4.3: 6 residues within 4Å: Chain A: T.49, D.148, R.155, S.156, R.158, H.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.148 Salt bridges: A:R.155, A:R.158, A:H.174 SO4.4: 8 residues within 4Å: Chain A: E.258, W.290, G.292, E.293, R.294, K.316, R.347, H.379 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.293 Salt bridges: A:R.294, A:K.316, A:R.347, A:H.379 SO4.12: 6 residues within 4Å: Chain B: G.292, E.293, R.294, K.316, R.347, H.379 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.293, B:R.294 Salt bridges: B:K.316, B:R.347, B:H.379 SO4.13: 5 residues within 4Å: Chain B: R.145, S.146, A.147, R.294, K.390 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.146, B:A.147, B:R.294 Salt bridges: B:R.145 SO4.21: 5 residues within 4Å: Chain C: R.145, S.146, A.147, R.294, K.390 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.146, C:A.147 Salt bridges: C:R.145, C:R.294, C:K.390 SO4.22: 6 residues within 4Å: Chain C: T.49, D.148, R.155, S.156, R.158, H.174 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.148 Salt bridges: C:R.155, C:R.158, C:H.174 SO4.23: 8 residues within 4Å: Chain C: E.258, W.290, G.292, E.293, R.294, K.316, R.347, H.379 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.293 Salt bridges: C:R.294, C:K.316, C:R.347, C:H.379 SO4.31: 6 residues within 4Å: Chain D: G.292, E.293, R.294, K.316, R.347, H.379 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.293, D:R.294 Salt bridges: D:K.316, D:R.347, D:H.379 SO4.32: 5 residues within 4Å: Chain D: R.145, S.146, A.147, R.294, K.390 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.146, D:A.147, D:R.294 Salt bridges: D:R.145

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: R.76, Q.80, P.130, V.131, V.132, K.133, E.252, Y.254 Ligands: TRP.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:V.131, A:E.252, W.7 GOL.6: 10 residues within 4Å: Chain A: E.73, M.190, V.193, R.194, T.197, A.251, E.252, I.253, Y.254, H.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.194, A:T.197, A:I.253, A:I.253, A:H.287 GOL.14: 4 residues within 4Å: Chain B: S.146, A.147, D.148, I.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.148 GOL.15: 7 residues within 4Å: Chain B: L.40, A.44, Q.47, R.59, L.262, D.263, R.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.263, B:R.266 GOL.16: 3 residues within 4Å: Chain B: R.35, Q.307, V.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.35, B:R.35 Water bridges: B:Q.307 GOL.24: 9 residues within 4Å: Chain C: R.76, Q.80, P.130, V.131, V.132, K.133, E.252, Y.254 Ligands: TRP.26 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: W.26, C:V.131 GOL.25: 10 residues within 4Å: Chain C: E.73, M.190, V.193, R.194, T.197, A.251, E.252, I.253, Y.254, H.287 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.194, C:T.197, C:I.253, C:I.253, C:H.287 GOL.33: 4 residues within 4Å: Chain D: S.146, A.147, D.148, I.149 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.148 GOL.34: 7 residues within 4Å: Chain D: L.40, A.44, Q.47, R.59, L.262, D.263, R.266 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.263, D:R.266 GOL.35: 3 residues within 4Å: Chain D: R.35, Q.307, V.308 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.35, D:R.35 Water bridges: D:Q.307

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.7: 17 residues within 4Å: Chain A: L.117, A.120, V.121, T.124, K.133, A.202, S.203, L.204, V.207, N.247, L.248, Q.249, T.250, A.251, E.252 Chain C: C.241 Ligands: GOL.5 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.121, A:L.204 Hydrogen bonds: A:A.202, A:L.204, A:N.247, A:N.247, W.7 Salt bridges: A:K.133 TRP.18: 16 residues within 4Å: Chain B: L.117, A.120, V.121, T.124, K.133, A.202, S.203, L.204, V.207, N.247, L.248, Q.249, T.250, A.251, E.252 Chain D: C.241 8 PLIP interactions: 2 Ligand-Ligand interactions, 6 interactions with chain B Hydrogen bonds: W.18, W.18, B:A.202, B:N.247, B:T.250 Hydrophobic interactions: B:V.121 Water bridges: B:K.133 Salt bridges: B:K.133 TRP.26: 17 residues within 4Å: Chain A: C.241 Chain C: L.117, A.120, V.121, T.124, K.133, A.202, S.203, L.204, V.207, N.247, L.248, Q.249, T.250, A.251, E.252 Ligands: GOL.24 8 PLIP interactions: 7 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:V.121, C:L.204 Hydrogen bonds: C:A.202, C:L.204, C:N.247, C:N.247, W.26 Salt bridges: C:K.133 TRP.37: 16 residues within 4Å: Chain B: C.241 Chain D: L.117, A.120, V.121, T.124, K.133, A.202, S.203, L.204, V.207, N.247, L.248, Q.249, T.250, A.251, E.252 8 PLIP interactions: 6 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:V.121 Hydrogen bonds: D:A.202, D:N.247, D:T.250, W.37, W.37 Water bridges: D:K.133 Salt bridges: D:K.133

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 6 residues within 4Å: Chain A: C.97, R.136, H.379, R.392, E.421, D.451 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.97, A:H.379, A:E.421, A:D.451, H2O.1 MN.11: 6 residues within 4Å: Chain B: C.97, R.136, H.379, R.392, E.421, D.451 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:H.379, B:E.421, B:D.451 MN.27: 6 residues within 4Å: Chain C: C.97, R.136, H.379, R.392, E.421, D.451 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.97, C:H.379, C:E.421, C:D.451, H2O.2 MN.30: 6 residues within 4Å: Chain D: C.97, R.136, H.379, R.392, E.421, D.451 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.97, D:H.379, D:E.421, D:D.451

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.9: 16 residues within 4Å: Chain A: F.101, M.102, N.104, R.181, A.184, N.185, A.188 Chain B: W.13, V.15, D.16, V.61, V.65, P.66, V.180, Y.183, A.184 9 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: F.9, A:F.101, A:N.185, A:N.185 Hydrophobic interactions: B:W.13, B:V.65, B:Y.183, A:A.184 Salt bridges: A:R.181 PHE.19: 14 residues within 4Å: Chain A: I.19, V.61, V.65, P.66, V.180, Y.183, A.184 Chain B: W.13, F.101, N.104, R.181, A.184, N.185, A.188 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:V.65, A:Y.183, B:A.184 Hydrogen bonds: B:F.101, B:N.185 Salt bridges: B:R.181 PHE.28: 16 residues within 4Å: Chain C: F.101, M.102, N.104, R.181, A.184, N.185, A.188 Chain D: W.13, V.15, D.16, V.61, V.65, P.66, V.180, Y.183, A.184 9 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:W.13, D:V.65, D:Y.183, C:A.184 Hydrogen bonds: C:F.101, C:N.185, C:N.185, F.28 Salt bridges: C:R.181 PHE.38: 14 residues within 4Å: Chain C: I.19, V.61, V.65, P.66, V.180, Y.183, A.184 Chain D: W.13, F.101, N.104, R.181, A.184, N.185, A.188 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C, Hydrophobic interactions: D:A.184, C:V.65, C:Y.183 Hydrogen bonds: D:F.101, D:N.185 Salt bridges: D:R.181

2 x TYR: TYROSINE(Non-covalent)

TYR.17: 14 residues within 4Å: Chain B: L.25, P.26, P.27, L.28, R.33, L.36, E.63, R.266, A.267, L.269, R.270, L.271, L.281 Ligands: CL.10 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.28, B:L.28, B:L.28, B:L.36 Hydrogen bonds: B:P.26, B:R.266, B:R.266, Y.17, Y.17 Salt bridges: B:R.33, B:R.266 TYR.36: 14 residues within 4Å: Chain D: L.25, P.26, P.27, L.28, R.33, L.36, E.63, R.266, A.267, L.269, R.270, L.271, L.281 Ligands: CL.29 11 PLIP interactions: 9 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:L.28, D:L.28, D:L.28 Hydrogen bonds: D:P.26, D:E.63, D:R.266, D:R.266, Y.36, Y.36 Salt bridges: D:R.33, D:R.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munack, S. et al., Remote Control by Inter-Enzyme Allostery: A Novel Paradigm for Regulation of the Shikimate Pathway. J.Mol.Biol. (2016)

Release Date

2016-01-27

Peptides

Phospho-2-dehydro-3-deoxyheptonate aldolase AroG: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Phospho-2-dehydro-3-deoxyheptonate aldolase AroG

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