SMTL ID : 4s38.1

IspG in complex MEcPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

CDI.1: 16 residues within 4Å: Chain A: P.298, V.345, N.346 Chain B: M.29, R.56, D.87, H.89, R.110, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Ligands: SF4.2 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:H.89, B:R.110, B:R.110, B:N.112, B:N.145, B:E.232, B:S.262, B:S.262 Water bridges: B:R.141, 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 CDI.10: 16 residues within 4Å: Chain A: M.29, R.56, D.87, H.89, R.110, R.141, N.145, K.204, T.231, E.232, R.260, S.262 Chain B: P.298, V.345, N.346 Ligands: SF4.11 21 PLIP interactions: 21 interactions with chain A 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 Water bridges: A:R.141, 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

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

SF4.2: 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.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.297, A:C.300, A:C.343 Salt bridges: B:E.232, B:E.232 SF4.11: 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.10 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, Salt bridges: A:E.232, A:E.232 Metal complexes: B:C.297, B:C.300, B:C.343

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

MES.3: 9 residues within 4Å: Chain A: E.280, Q.283, F.290, A.291, P.292, E.293, V.294, S.316 Chain B: K.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.294, A:S.316, A:S.316 Salt bridges: A:E.280 MES.12: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.294, B:S.316, B:S.316 Salt bridges: B:E.280

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: T.379, L.381, E.389, R.392, L.393 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.389, A:R.392, A:R.392 GOL.5: 8 residues within 4Å: Chain A: N.31, P.265, A.266, G.268, E.269, P.270, R.271 Chain B: Q.309 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.309, A:N.31, A:A.266, A:G.268, A:E.269 Water bridges: A:Q.43 GOL.6: 5 residues within 4Å: Chain A: R.49, A.50, Q.279, A.291, R.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.279, A:R.327 GOL.13: 5 residues within 4Å: Chain B: T.379, L.381, E.389, R.392, L.393 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.379, B:E.389, B:R.392, B:R.392 GOL.14: 8 residues within 4Å: Chain A: Q.309 Chain B: N.31, P.265, A.266, G.268, E.269, P.270, R.271 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.31, B:A.266, B:G.268, B:E.269, A:Q.309 Water bridges: B:Q.43 GOL.15: 5 residues within 4Å: Chain B: R.49, A.50, Q.279, A.291, R.327 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.279, B:R.327

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

PEG.7: 4 residues within 4Å: Chain A: K.352, Y.372, K.376, L.377 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.352, A:Y.372, A:L.377 PEG.8: 3 residues within 4Å: Chain A: A.127, R.131, M.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.131 Water bridges: A:A.127 PEG.16: 4 residues within 4Å: Chain B: K.352, Y.372, K.376, L.377 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.352, B:L.377 PEG.17: 3 residues within 4Å: Chain B: A.127, R.131, M.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.131 Water bridges: B:A.127

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 6 residues within 4Å: Chain A: Y.186, E.187, L.190, E.191, E.196, Q.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.196 Water bridges: A:G.193, A:Q.223 1PE.18: 6 residues within 4Å: Chain B: Y.186, E.187, L.190, E.191, E.196, Q.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.186, B:E.196 Water bridges: B:G.193, B:Q.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quitterer, F. et al., Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE). J.Mol.Biol. (2015)

Release Date

2015-04-29

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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