SMTL ID : 1vha.3 (2 other biounits)

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-12-mer

Ligands

10 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: D.11, V.12 Chain B: E.138 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, H2O.2 MN.3: 3 residues within 4Å: Chain B: D.11, V.12 Chain C: E.138 No protein-ligand interaction detected (PLIP) MN.6: 3 residues within 4Å: Chain A: E.138 Chain C: D.11, V.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.11 MN.8: 3 residues within 4Å: Chain D: D.11, V.12 Chain E: E.138 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.11, H2O.7 MN.10: 3 residues within 4Å: Chain E: D.11, V.12 Chain F: E.138 No protein-ligand interaction detected (PLIP) MN.13: 3 residues within 4Å: Chain D: E.138 Chain F: D.11, V.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.11 MN.15: 3 residues within 4Å: Chain G: D.11, V.12 Chain H: E.138 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.11, H2O.11 MN.19: 2 residues within 4Å: Chain G: E.138 Chain I: V.12 No protein-ligand interaction detected (PLIP) MN.21: 3 residues within 4Å: Chain J: D.11, V.12 Chain K: E.138 2 PLIP interactions: 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.11, H2O.15 MN.25: 2 residues within 4Å: Chain J: E.138 Chain L: V.12 No protein-ligand interaction detected (PLIP)

12 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 8 residues within 4Å: Chain A: L.140, G.141, F.142, T.143 Chain C: F.142 Ligands: POP.4, ACY.5, ACY.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.143 ACY.5: 8 residues within 4Å: Chain B: T.137, L.140, G.141, F.142, T.143 Ligands: ACY.2, POP.4, ACY.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.143 Hydrogen bonds: B:T.143 ACY.7: 9 residues within 4Å: Chain B: F.142 Chain C: T.137, L.140, G.141, F.142, T.143 Ligands: ACY.2, POP.4, ACY.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.137, C:T.143 Hydrogen bonds: C:T.143 ACY.9: 8 residues within 4Å: Chain D: L.140, G.141, F.142, T.143 Chain F: F.142 Ligands: POP.11, ACY.12, ACY.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.143 ACY.12: 8 residues within 4Å: Chain E: T.137, L.140, G.141, F.142, T.143 Ligands: ACY.9, POP.11, ACY.14 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.143 Hydrogen bonds: E:T.143 ACY.14: 9 residues within 4Å: Chain E: F.142 Chain F: T.137, L.140, G.141, F.142, T.143 Ligands: ACY.9, POP.11, ACY.12 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.137, F:T.143 Hydrogen bonds: F:T.143 ACY.17: 7 residues within 4Å: Chain G: G.141, F.142, T.143 Chain I: F.142 Ligands: POP.16, ACY.18, ACY.20 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:F.142, G:T.143 ACY.18: 9 residues within 4Å: Chain G: F.142 Chain H: T.137, L.140, G.141, F.142, T.143 Ligands: POP.16, ACY.17, ACY.20 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:T.143 ACY.20: 9 residues within 4Å: Chain H: F.142 Chain I: T.137, L.140, G.141, F.142, T.143 Ligands: POP.16, ACY.17, ACY.18 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:T.137, I:T.143 Hydrogen bonds: I:T.137, I:T.143 ACY.23: 7 residues within 4Å: Chain J: G.141, F.142, T.143 Chain L: F.142 Ligands: POP.22, ACY.24, ACY.26 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:F.142, J:T.143 ACY.24: 9 residues within 4Å: Chain J: F.142 Chain K: T.137, L.140, G.141, F.142, T.143 Ligands: POP.22, ACY.23, ACY.26 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.143 ACY.26: 9 residues within 4Å: Chain K: F.142 Chain L: T.137, L.140, G.141, F.142, T.143 Ligands: POP.22, ACY.23, ACY.24 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:T.137, L:T.143 Hydrogen bonds: L:T.137, L:T.143

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

POP.4: 12 residues within 4Å: Chain A: G.141, F.142, R.145 Chain B: G.141, F.142, R.145 Chain C: G.141, F.142, R.145 Ligands: ACY.2, ACY.5, ACY.7 10 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:F.142, A:G.141, A:F.142, C:F.142 Salt bridges: B:R.145, A:R.145, C:R.145 Water bridges: A:R.145, A:E.147, C:R.145 POP.11: 12 residues within 4Å: Chain D: G.141, F.142, R.145 Chain E: G.141, F.142, R.145 Chain F: G.141, F.142, R.145 Ligands: ACY.9, ACY.12, ACY.14 10 PLIP interactions: 3 interactions with chain F, 5 interactions with chain D, 2 interactions with chain E Hydrogen bonds: F:F.142, D:G.141, D:F.142, E:F.142 Water bridges: F:R.145, D:R.145, D:E.147 Salt bridges: F:R.145, D:R.145, E:R.145 POP.16: 12 residues within 4Å: Chain G: G.141, F.142, R.145 Chain H: G.141, F.142, R.145 Chain I: G.141, F.142, R.145 Ligands: ACY.17, ACY.18, ACY.20 11 PLIP interactions: 3 interactions with chain I, 5 interactions with chain G, 3 interactions with chain H Hydrogen bonds: I:F.142, G:G.141, G:F.142, H:G.141, H:F.142 Water bridges: I:E.147, G:R.145, G:R.145 Salt bridges: I:R.145, G:R.145, H:R.145 POP.22: 12 residues within 4Å: Chain J: G.141, F.142, R.145 Chain K: G.141, F.142, R.145 Chain L: G.141, F.142, R.145 Ligands: ACY.23, ACY.24, ACY.26 11 PLIP interactions: 5 interactions with chain J, 3 interactions with chain L, 3 interactions with chain K Hydrogen bonds: J:G.141, J:F.142, L:F.142, K:G.141, K:F.142 Water bridges: J:R.145, J:R.145, L:E.147 Salt bridges: J:R.145, L:R.145, K:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badger, J. et al., Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins (2005)

Release Date

2003-12-30

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
A

E
B

F
C

G
D

H
E

I
F

J
D

K
E

L
F

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

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