SMTL ID : 5ckx.1

Non-covalent complex of DAHP synthase and chorismate mutase from Mycobacterium tuberculosis with bound transition state analog and feedback effectors tyrosine and phenylalanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-4-mer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: C.97, R.136, H.379, R.392, E.421, D.451 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:H.379, A:E.421, A:D.451 MN.10: 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:E.421 MN.24: 6 residues within 4Å: Chain E: C.97, R.136, H.379, R.392, E.421, D.451 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.97, E:H.379, E:E.421, E:D.451 MN.33: 6 residues within 4Å: Chain F: C.97, R.136, H.379, R.392, E.421, D.451 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.97, F:H.379, F:E.421, F:E.421

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.73, A:T.197, A:I.253, A:H.287 GOL.11: 11 residues within 4Å: Chain B: E.73, R.76, M.190, V.193, R.194, T.197, A.251, E.252, I.253, Y.254, H.287 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.73, B:E.73, B:R.76, B:R.76, B:T.197, B:I.253, B:I.253 GOL.12: 10 residues within 4Å: Chain B: A.120, V.121, T.124, P.130, V.131, K.133, L.204 Chain F: A.240, C.241 Ligands: GOL.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:V.131, B:K.133, F:A.240 GOL.13: 9 residues within 4Å: Chain B: Q.80, A.89, P.130, V.131, V.132, K.133, E.252, Y.254 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.131 Water bridges: B:E.252 GOL.21: 4 residues within 4Å: Chain D: R.46, V.55 Chain H: I.14, R.18 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:R.46, H:R.18 GOL.25: 10 residues within 4Å: Chain E: E.73, M.190, V.193, R.194, T.197, A.251, E.252, I.253, Y.254, H.287 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.73, E:T.197, E:I.253, E:H.287 GOL.34: 11 residues within 4Å: Chain F: E.73, R.76, M.190, V.193, R.194, T.197, A.251, E.252, I.253, Y.254, H.287 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.73, F:R.76, F:R.76, F:T.197, F:I.253, F:I.253 GOL.35: 10 residues within 4Å: Chain B: A.240, C.241 Chain F: A.120, V.121, T.124, P.130, V.131, K.133, L.204 Ligands: GOL.36 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:V.131, F:K.133, B:A.240 GOL.36: 9 residues within 4Å: Chain F: Q.80, A.89, P.130, V.131, V.132, K.133, E.252, Y.254 Ligands: GOL.35 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.131, F:E.252 Water bridges: F:E.252 GOL.44: 4 residues within 4Å: Chain D: I.14, R.18 Chain H: R.46, V.55 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:R.18, H:R.46

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

CL.3: 2 residues within 4Å: Chain A: A.45, Q.46 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: D.160, G.164, F.165, R.178, R.181 Chain B: D.16 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: R.110 Chain B: V.70, P.71, S.72 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain E: A.45, Q.46 Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain E: D.160, G.164, F.165, R.178, R.181 Chain F: D.16 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain E: R.110 Chain F: V.70, P.71, S.72 Ligand excluded by PLIP

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

SO4.5: 6 residues within 4Å: Chain A: G.292, E.293, R.294, K.316, R.347, H.379 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.471, D.472 Chain C: R.82, R.87 Chain E: R.233 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: R.145, S.146, A.147, R.294 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: V.70, P.71, S.72 Chain B: R.110, S.199 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain B: G.292, E.293, R.294, K.316, R.347, H.379 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: R.145, S.146, A.147, R.294, K.390 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: V.55, S.57, R.58 Chain G: R.18 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: R.471, D.472 Chain D: R.82, R.87 Chain F: R.233 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain E: G.292, E.293, R.294, K.316, R.347, H.379 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain A: R.233 Chain E: R.471, D.472 Chain G: R.82, R.87 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain E: R.145, S.146, A.147, R.294 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain E: V.70, P.71, S.72 Chain F: R.110, S.199 Ligand excluded by PLIP SO4.38: 6 residues within 4Å: Chain F: G.292, E.293, R.294, K.316, R.347, H.379 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain F: R.145, S.146, A.147, R.294, K.390 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: R.18 Chain G: V.55, S.57, R.58 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain B: R.233 Chain F: R.471, D.472 Chain H: R.82, R.87 Ligand excluded by PLIP

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 11 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.184, A:A.188, B:W.13, B:V.65 Hydrogen bonds: A:N.185, A:N.185, A:N.185, B:D.16, F.9 Salt bridges: A:R.181 pi-Stacking: B:Y.183 PHE.17: 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: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.184, A:V.65 Hydrogen bonds: B:F.101, B:N.185 Salt bridges: B:R.181 pi-Stacking: A:Y.183 PHE.32: 16 residues within 4Å: Chain E: F.101, M.102, N.104, R.181, A.184, N.185, A.188 Chain F: W.13, V.15, D.16, V.61, V.65, P.66, V.180, Y.183, A.184 11 PLIP interactions: 6 interactions with chain E, 4 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: E:A.184, E:A.188, F:W.13, F:V.65 Hydrogen bonds: E:N.185, E:N.185, E:N.185, F:D.16, F.32 Salt bridges: E:R.181 pi-Stacking: F:Y.183 PHE.40: 14 residues within 4Å: Chain E: I.19, V.61, V.65, P.66, V.180, Y.183, A.184 Chain F: W.13, F.101, N.104, R.181, A.184, N.185, A.188 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E, Hydrophobic interactions: F:A.184, E:V.65 Hydrogen bonds: F:F.101, F:N.185 Salt bridges: F:R.181 pi-Stacking: E:Y.183

2 x TYR: TYROSINE(Non-covalent)

TYR.18: 14 residues within 4Å: Chain B: L.25, P.26, P.27, L.28, R.33, L.36, R.59, E.63, R.266, A.267, L.269, R.270, L.271, L.281 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.28, B:L.28, B:L.28, B:L.36 Hydrogen bonds: B:P.26, B:E.63, B:R.266, Y.18 Salt bridges: B:R.33, B:R.59, B:R.266 TYR.41: 14 residues within 4Å: Chain F: L.25, P.26, P.27, L.28, R.33, L.36, R.59, E.63, R.266, A.267, L.269, R.270, L.271, L.281 12 PLIP interactions: 11 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:L.28, F:L.28, F:L.28, F:L.36 Hydrogen bonds: F:P.26, F:E.63, F:E.63, F:R.266, Y.41 Salt bridges: F:R.33, F:R.59, F:R.266

4 x TSA: 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID(Non-covalent)

TSA.20: 16 residues within 4Å: Chain C: R.35, S.39, I.42, G.43, R.46, R.53, L.54, V.55, R.58, E.59, V.62, L.81, G.84, R.85 Chain G: R.18, I.21 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:R.58, C:E.59, C:R.85 Hydrogen bonds: C:R.46, C:R.46, C:V.55, C:V.55, C:E.59 Salt bridges: C:R.35, C:R.46, C:R.58, G:R.18 TSA.23: 15 residues within 4Å: Chain D: R.35, S.39, I.42, R.46, R.53, L.54, V.55, R.58, E.59, V.62, L.81, G.84, R.85 Chain H: R.18, I.21 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: D:R.58, D:E.59, D:R.85 Hydrogen bonds: D:S.39, D:R.46, D:V.55, D:V.55 Salt bridges: D:R.35, D:R.46, D:R.58, H:R.18 TSA.43: 16 residues within 4Å: Chain C: R.18, I.21 Chain G: R.35, S.39, I.42, G.43, R.46, R.53, L.54, V.55, R.58, E.59, V.62, L.81, G.84, R.85 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:R.58, G:E.59, G:R.85 Hydrogen bonds: G:R.46, G:R.46, G:V.55, G:V.55 Salt bridges: G:R.35, G:R.46, G:R.58, C:R.18 TSA.46: 15 residues within 4Å: Chain D: R.18, I.21 Chain H: R.35, S.39, I.42, R.46, R.53, L.54, V.55, R.58, E.59, V.62, L.81, G.84, R.85 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain H Salt bridges: D:R.18, H:R.35, H:R.46, H:R.58 Hydrophobic interactions: H:R.58, H:E.59, H:R.85 Hydrogen bonds: H:S.39, H:R.46, H:V.55, H:V.55, H:E.59

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

2016-03-16

Peptides

Phospho-2-dehydro-3-deoxyheptonate aldolase AroG: ABEF
Intracellular chorismate mutase: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

Phospho-2-dehydro-3-deoxyheptonate aldolase AroG

Intracellular chorismate mutase

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