SMTL ID : 4g9p.1

Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: C.297, P.298, G.299, C.300, R.302, T.303, M.341, G.342, C.343, V.345, N.346 Ligands: CDI.9 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, Salt bridges: B:E.232, B:E.232 Metal complexes: A:C.297, A:C.300, A:C.343 SF4.8: 12 residues within 4Å: Chain B: C.297, P.298, G.299, C.300, R.302, T.303, M.341, G.342, C.343, V.345, N.346 Ligands: CDI.2 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.297, B:C.300, B:C.343 Salt bridges: A:E.232, A:E.232

2 x CDI: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE(Non-covalent)

CDI.2: 18 residues within 4Å: Chain A: M.29, R.56, D.87, H.89, R.110, N.112, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Chain B: C.297, P.298, V.345, N.346 Ligands: SF4.8 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.89, A:R.110, A:R.110, A:N.112, A:N.145, A:T.231, A:E.232, A:S.262, A:S.262, B:N.346 Water bridges: A:R.141, A:K.204, A:K.204, A:R.260 Salt bridges: A:R.56, A:R.56, A:R.110, A:R.141, A:K.204, A:K.204, A:R.260 CDI.9: 18 residues within 4Å: Chain A: C.297, P.298, V.345, N.346 Chain B: M.29, R.56, D.87, H.89, R.110, N.112, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Ligands: SF4.1 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.89, B:R.110, B:R.110, B:N.112, B:N.145, B:T.231, B:E.232, B:S.262, B:S.262, A:N.346 Water bridges: B:R.141, B:K.204, B:K.204, B:R.260 Salt bridges: B:R.56, B:R.56, B:R.110, B:R.141, B:K.204, B:K.204, B:R.260

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 12 residues within 4Å: Chain A: Q.279, E.280, Q.283, F.290, A.291, P.292, E.293, V.294, S.316, L.319 Chain B: M.235, K.238 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.294, A:S.316, A:S.316 Water bridges: A:E.280, B:K.238 Salt bridges: A:E.280 MES.6: 7 residues within 4Å: Chain A: P.113, L.116, K.122, D.123, F.126, A.185, A.188 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.185 Salt bridges: A:D.123 MES.10: 12 residues within 4Å: Chain A: M.235, K.238 Chain B: Q.279, E.280, Q.283, F.290, A.291, P.292, E.293, V.294, S.316, L.319 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.294, B:S.316, B:S.316 Salt bridges: B:E.280 Water bridges: A:K.238 MES.13: 7 residues within 4Å: Chain B: P.113, L.116, K.122, D.123, F.126, A.185, A.188 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.185 Salt bridges: B:D.123

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

CL.4: 5 residues within 4Å: Chain A: N.31, P.265, R.271 Chain B: Q.309 Ligands: K.5 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: Q.27, S.28, M.29, R.56, H.227, R.260 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: Q.309 Chain B: N.31, P.265, R.271 Ligands: K.12 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: Q.27, S.28, M.29, R.56, H.227, R.260 Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: P.265, S.266, P.267, E.269 Chain B: Q.309 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.266, A:E.269 K.12: 6 residues within 4Å: Chain A: Q.309 Chain B: P.265, S.266, P.267, E.269 Ligands: CL.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.266, B:E.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rekittke, I. et al., Structure of the GcpE (IspG)-MEcPP complex from Thermus thermophilus. Febs Lett. (2012)

Release Date

2012-09-26

Peptides

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase

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