SMTL ID : 6mwk.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0883

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.14, H.16, H.48 Ligands: K4Y.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.14, A:H.16, A:H.48, H2O.1 ZN.6: 4 residues within 4Å: Chain B: D.14, H.16, H.48 Ligands: K4Y.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.14, B:D.14, B:H.16, B:H.48 ZN.10: 4 residues within 4Å: Chain C: D.14, H.16, H.48 Ligands: K4Y.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.14, C:H.16, C:H.48

3 x K4Y: 4-amino-N-(6-methoxypyrimidin-4-yl)benzene-1-sulfonamide(Non-covalent)

K4Y.2: 15 residues within 4Å: Chain A: D.14, H.16, G.39, H.40, S.41, H.48, I.63, G.64, F.67, S.68, D.69, F.74, L.82 Chain B: K.138 Ligands: ZN.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.40, A:D.69, A:F.74, A:L.82 Hydrogen bonds: A:H.40, A:S.41, A:S.68, B:K.138 Water bridges: A:I.63, A:G.64 K4Y.7: 11 residues within 4Å: Chain B: D.14, H.16, G.39, H.40, H.48, I.63, G.64, F.67, L.82 Chain C: K.138 Ligands: ZN.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:H.40, B:L.82 Hydrogen bonds: B:H.40, B:F.67, C:K.138 Water bridges: B:S.41, B:G.64 K4Y.11: 11 residues within 4Å: Chain A: K.138 Chain C: D.14, H.16, G.39, H.40, H.48, I.63, G.64, F.67, L.82 Ligands: ZN.10 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.82 Hydrogen bonds: C:H.40, C:F.67, A:K.138 Water bridges: C:A.43, C:G.64, A:E.141

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 8 residues within 4Å: Chain A: A.106, Q.107, A.108, P.109, K.110, L.111, K.138, T.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.111, A:A.112 DMS.4: 3 residues within 4Å: Chain A: A.91, Q.92, G.94 No protein-ligand interaction detected (PLIP) DMS.8: 6 residues within 4Å: Chain B: A.106, P.109, K.110, L.111, A.112, A.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.111, B:A.112 DMS.12: 9 residues within 4Å: Chain C: A.106, Q.107, P.109, K.110, L.111, A.112, A.137, K.138, T.139 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.111, C:A.112

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x MLA: MALONIC ACID(Non-covalent)

MLA.9: 9 residues within 4Å: Chain A: G.144, Y.145, R.148 Chain B: G.144, Y.145, R.148 Chain C: G.144, Y.145, R.148 14 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:Y.145 Hydrogen bonds: C:Y.145, A:Y.145, B:Y.145 Water bridges: C:G.144, C:R.148, A:G.144, A:G.144, A:Y.145, A:R.148, B:R.148 Salt bridges: C:R.148, A:R.148, B:R.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456. To Be Published

Release Date

2019-11-06

Peptides

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Related Entries With Identical Sequence