SMTL ID : 4s23.1

Structure of the GcpE-HMBPP complex from Thermus thermophilius

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.297, P.298, G.299, C.300, R.302, T.303, M.341, G.342, C.343, N.346 Ligands: H6P.6 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:C.297, A:C.300, A:C.343, H2O.10 Salt bridges: B:E.232, B:E.232 SF4.4: 11 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 Ligands: H6P.3 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions, Metal complexes: B:C.297, B:C.300, B:C.343, H2O.1, H2O.57 Salt bridges: A:E.232, A:E.232

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

MES.2: 9 residues within 4Å: Chain A: Q.279, E.280, Q.283, A.291, P.292, E.293, V.294, S.316 Chain B: K.238 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.294, A:S.316, A:S.316 Salt bridges: A:E.280 Water bridges: B:M.235 MES.5: 9 residues within 4Å: Chain A: K.238 Chain B: E.280, Q.283, F.290, A.291, P.292, E.293, V.294, S.316 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:M.235 Hydrogen bonds: B:V.294, B:S.316, B:S.316 Salt bridges: B:E.280

2 x H6P: (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate(Non-covalent)

H6P.3: 14 residues within 4Å: Chain A: R.56, D.87, H.89, R.110, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Chain B: V.345, N.346 Ligands: SF4.4 20 PLIP interactions: 19 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:E.232, A:S.262, B:N.346 Water bridges: A:R.141, A:R.141, A:K.204, A:R.260, A:S.262 Salt bridges: A:R.56, A:R.56, A:R.110, A:R.141, A:K.204, A:K.204, A:R.260 H6P.6: 13 residues within 4Å: Chain A: N.346 Chain B: R.56, D.87, H.89, R.110, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Ligands: SF4.1 19 PLIP interactions: 1 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:N.346, B:R.110, B:R.110, B:N.112, B:N.145, B:T.231, B:E.232, B:S.262 Water bridges: B:R.141, B:R.141, B:R.260, B:S.262 Salt bridges: B:R.56, B:R.56, B:R.110, B:R.141, B:K.204, B:K.204, B:R.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rekittke, I. et al., Structure of the GcpE-HMBPP complex from Thermus thermophilius. Biochem.Biophys.Res.Commun. (2015)

Release Date

2015-03-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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