SMTL ID : 3re3.3 (2 other biounits)

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-12-mer

Ligands

6 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.1: 9 residues within 4Å: Chain A: T.139, E.141 Chain E: D.13, V.14, H.15, G.43, D.44, V.45, H.48 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.13, E:V.14, E:V.14, A:T.139 Water bridges: E:D.13 Salt bridges: E:H.48, E:H.48 POP.5: 10 residues within 4Å: Chain B: D.13, V.14, H.15, D.42, G.43, V.45, H.48 Chain C: T.138, T.139, E.141 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.13, B:V.14, C:E.141 Water bridges: B:D.44, C:T.139, C:T.139 Salt bridges: B:H.48, B:H.48 POP.13: 9 residues within 4Å: Chain E: T.139, E.141 Chain I: D.13, V.14, H.15, G.43, D.44, V.45, H.48 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain E Hydrogen bonds: I:D.13, I:V.14, I:V.14, E:T.139 Water bridges: I:D.13 Salt bridges: I:H.48, I:H.48 POP.17: 10 residues within 4Å: Chain F: D.13, V.14, H.15, D.42, G.43, V.45, H.48 Chain G: T.138, T.139, E.141 8 PLIP interactions: 3 interactions with chain G, 5 interactions with chain F Hydrogen bonds: G:E.141, F:D.13, F:V.14 Water bridges: G:T.139, G:T.139, F:D.44 Salt bridges: F:H.48, F:H.48 POP.25: 9 residues within 4Å: Chain A: D.13, V.14, H.15, G.43, D.44, V.45, H.48 Chain I: T.139, E.141 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:D.13, A:V.14, A:V.14, I:T.139 Water bridges: A:D.13 Salt bridges: A:H.48, A:H.48 POP.29: 10 residues within 4Å: Chain J: D.13, V.14, H.15, D.42, G.43, V.45, H.48 Chain K: T.138, T.139, E.141 8 PLIP interactions: 5 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:D.13, J:V.14, K:E.141 Water bridges: J:D.44, K:T.139, K:T.139 Salt bridges: J:H.48, J:H.48

9 x NA: SODIUM ION(Non-functional Binders)

NA.2: 8 residues within 4Å: Chain A: R.7, G.56, A.57, G.59 Chain I: N.99, I.100, Q.132, N.134 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain A Hydrogen bonds: I:I.100, I:Q.132, I:N.134, A:R.7, A:G.59 NA.6: 7 residues within 4Å: Chain B: N.99, I.100, Q.132, N.134 Chain D: R.7, G.56, A.57 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.99, B:I.100, B:Q.132, B:N.134, D:R.7 NA.9: 8 residues within 4Å: Chain C: R.7, G.56, A.57 Chain D: N.99, I.100, S.131, Q.132, N.134 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.99, D:I.100, D:N.134, C:G.56, C:G.59 NA.14: 8 residues within 4Å: Chain A: N.99, I.100, Q.132, N.134 Chain E: R.7, G.56, A.57, G.59 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:R.7, E:G.59, A:N.99, A:I.100, A:N.134 NA.18: 7 residues within 4Å: Chain F: N.99, I.100, Q.132, N.134 Chain H: R.7, G.56, A.57 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:N.99, F:I.100, F:Q.132, F:N.134, H:R.7 NA.21: 8 residues within 4Å: Chain G: R.7, G.56, A.57 Chain H: N.99, I.100, S.131, Q.132, N.134 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:N.99, H:I.100, H:Q.132, H:N.134, G:G.59 NA.26: 8 residues within 4Å: Chain E: N.99, I.100, Q.132, N.134 Chain I: R.7, G.56, A.57, G.59 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain I Hydrogen bonds: E:I.100, E:I.100, E:N.134, I:R.7, I:G.59 NA.30: 7 residues within 4Å: Chain J: N.99, I.100, Q.132, N.134 Chain L: R.7, G.56, A.57 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain J Hydrogen bonds: L:R.7, L:G.56, J:N.99, J:I.100, J:N.134 NA.33: 8 residues within 4Å: Chain K: R.7, G.56, A.57 Chain L: N.99, I.100, S.131, Q.132, N.134 5 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:G.56, K:G.59, L:N.99, L:I.100, L:N.134

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

CL.3: 8 residues within 4Å: Chain A: G.144, R.148 Chain E: R.148 Ligands: PO4.4, CL.15, PO4.16, CL.27, PO4.28 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: D.13, H.48 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain E: G.144, R.148 Chain I: R.148 Ligands: CL.3, PO4.4, PO4.16, CL.27, PO4.28 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain H: D.13, H.48 Ligand excluded by PLIP CL.27: 8 residues within 4Å: Chain A: R.148 Chain I: G.144, R.148 Ligands: CL.3, PO4.4, CL.15, PO4.16, PO4.28 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain L: D.13, H.48 Ligand excluded by PLIP

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 11 residues within 4Å: Chain A: G.144, F.145 Chain E: G.144, F.145 Chain I: G.144, F.145 Ligands: CL.3, CL.15, PO4.16, CL.27, PO4.28 6 PLIP interactions: 3 interactions with chain I, 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: I:F.145, A:F.145, E:F.145 Water bridges: I:G.144, I:I.146, A:I.146 PO4.7: 7 residues within 4Å: Chain B: Y.12, H.155 Chain C: Y.12, H.155 Chain D: Y.12, H.155 Ligands: MPD.8 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:Y.12, B:Y.12, D:Y.12 Salt bridges: C:H.155, B:H.155, D:H.155 PO4.11: 9 residues within 4Å: Chain B: G.144, F.145, R.148 Chain C: G.144, R.148 Chain D: G.144, F.145, R.148 Ligands: MPD.8 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:F.145, D:F.145, B:F.145 Salt bridges: C:R.148, D:R.148, B:R.148 Water bridges: D:R.148 PO4.16: 11 residues within 4Å: Chain A: G.144, F.145 Chain E: G.144, F.145 Chain I: G.144, F.145 Ligands: CL.3, PO4.4, CL.15, CL.27, PO4.28 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 1 interactions with chain I Hydrogen bonds: A:F.145, E:F.145, I:F.145 Water bridges: A:I.146, E:I.146 PO4.19: 7 residues within 4Å: Chain F: Y.12, H.155 Chain G: Y.12, H.155 Chain H: Y.12, H.155 Ligands: MPD.20 6 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H, 2 interactions with chain F Hydrogen bonds: G:Y.12, H:Y.12, F:Y.12 Salt bridges: G:H.155, H:H.155, F:H.155 PO4.23: 9 residues within 4Å: Chain F: G.144, F.145, R.148 Chain G: G.144, R.148 Chain H: G.144, F.145, R.148 Ligands: MPD.20 7 PLIP interactions: 3 interactions with chain H, 2 interactions with chain G, 2 interactions with chain F Hydrogen bonds: H:F.145, G:F.145, F:F.145 Water bridges: H:R.148 Salt bridges: H:R.148, G:R.148, F:R.148 PO4.28: 11 residues within 4Å: Chain A: G.144, F.145 Chain E: G.144, F.145 Chain I: G.144, F.145 Ligands: CL.3, PO4.4, CL.15, PO4.16, CL.27 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain I, 1 interactions with chain A Hydrogen bonds: E:F.145, I:F.145, A:F.145 Water bridges: E:I.146, I:I.146 PO4.31: 7 residues within 4Å: Chain J: Y.12, H.155 Chain K: Y.12, H.155 Chain L: Y.12, H.155 Ligands: MPD.32 6 PLIP interactions: 2 interactions with chain L, 2 interactions with chain J, 2 interactions with chain K Hydrogen bonds: L:Y.12, J:Y.12, K:Y.12 Salt bridges: L:H.155, J:H.155, K:H.155 PO4.35: 9 residues within 4Å: Chain J: G.144, F.145, R.148 Chain K: G.144, R.148 Chain L: G.144, F.145, R.148 Ligands: MPD.32 7 PLIP interactions: 2 interactions with chain K, 3 interactions with chain L, 2 interactions with chain J Hydrogen bonds: K:F.145, L:F.145, J:F.145 Salt bridges: K:R.148, L:R.148, J:R.148 Water bridges: L:R.148

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 7 residues within 4Å: Chain B: G.144, F.145 Chain C: G.144, F.145 Chain D: F.145 Ligands: PO4.7, PO4.11 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: C:F.145, C:F.145, D:F.145, B:F.145 Hydrogen bonds: B:F.145 Water bridges: B:L.143 MPD.10: 6 residues within 4Å: Chain C: D.13, V.14, H.48 Chain D: T.138, T.139, E.141 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.13, C:V.14, D:T.139, D:T.139 MPD.20: 7 residues within 4Å: Chain F: G.144, F.145 Chain G: G.144, F.145 Chain H: F.145 Ligands: PO4.19, PO4.23 6 PLIP interactions: 1 interactions with chain H, 3 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: H:F.145, F:F.145, G:F.145, G:F.145 Hydrogen bonds: F:F.145 Water bridges: F:L.143 MPD.22: 6 residues within 4Å: Chain G: D.13, V.14, H.48 Chain H: T.138, T.139, E.141 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:T.139, H:T.139, G:D.13, G:V.14 MPD.32: 7 residues within 4Å: Chain J: G.144, F.145 Chain K: G.144, F.145 Chain L: F.145 Ligands: PO4.31, PO4.35 6 PLIP interactions: 2 interactions with chain K, 3 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: K:F.145, K:F.145, J:F.145, L:F.145 Hydrogen bonds: J:F.145 Water bridges: J:L.143 MPD.34: 6 residues within 4Å: Chain K: D.13, V.14, H.48 Chain L: T.138, T.139, E.141 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:T.139, L:T.139, K:D.13, K:V.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis. To be Published

Release Date

2011-04-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

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

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