SMTL ID : 5ero.1 (3 other biounits)

Crystal structure of elongation domain of Phomopsis amygdali fusicoccadiene synthase complexed with cobalt ions and pamidronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

24 x CO: COBALT (II) ION(Non-covalent)

CO.1: 3 residues within 4Å: Chain A: D.235, K.259 Ligands: 210.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.235, H2O.1, H2O.1, H2O.1 CO.2: 4 residues within 4Å: Chain A: D.104, D.108 Ligands: CO.3, 210.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.104, A:D.108, H2O.1, H2O.1, H2O.1 CO.3: 4 residues within 4Å: Chain A: D.104, D.108 Ligands: CO.2, 210.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.104, A:D.108, H2O.1, H2O.2 CO.5: 1 residues within 4Å: Chain A: D.77 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.77 CO.6: 3 residues within 4Å: Chain B: D.235, K.259 Ligands: 210.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.235, H2O.4, H2O.4, H2O.4 CO.7: 5 residues within 4Å: Chain B: D.104, D.108, E.257 Ligands: CO.8, 210.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.104, B:D.108, H2O.3, H2O.3, H2O.3 CO.8: 4 residues within 4Å: Chain B: D.104, D.108 Ligands: CO.7, 210.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.104, B:D.108, H2O.3, H2O.3 CO.10: 1 residues within 4Å: Chain B: D.83 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.83 CO.11: 4 residues within 4Å: Chain C: D.235, D.236, D.254 Ligands: 210.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.235 CO.12: 5 residues within 4Å: Chain C: D.104, D.108, E.257 Ligands: CO.13, 210.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.104, C:D.108 CO.13: 6 residues within 4Å: Chain C: D.104, D.108, Q.166, E.257 Ligands: CO.12, 210.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.104, C:D.108, H2O.5, H2O.5 CO.15: 2 residues within 4Å: Chain C: D.73, D.77 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.77 CO.16: 3 residues within 4Å: Chain D: D.235, K.259 Ligands: 210.19 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.235, H2O.6, H2O.6, H2O.7 CO.17: 4 residues within 4Å: Chain D: D.104, D.108 Ligands: CO.18, 210.19 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.104, D:D.108, H2O.6, H2O.6, H2O.6 CO.18: 4 residues within 4Å: Chain D: D.104, D.108 Ligands: CO.17, 210.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.104, D:D.108, H2O.6, H2O.7 CO.20: 1 residues within 4Å: Chain D: D.77 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.77 CO.21: 3 residues within 4Å: Chain E: D.235, K.259 Ligands: 210.24 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.235, H2O.9, H2O.9, H2O.9 CO.22: 5 residues within 4Å: Chain E: D.104, D.108, E.257 Ligands: CO.23, 210.24 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.104, E:D.108, H2O.8, H2O.8, H2O.8 CO.23: 4 residues within 4Å: Chain E: D.104, D.108 Ligands: CO.22, 210.24 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.104, E:D.108, H2O.8, H2O.8 CO.25: 1 residues within 4Å: Chain E: D.83 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.83 CO.26: 4 residues within 4Å: Chain F: D.235, D.236, D.254 Ligands: 210.29 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.235 CO.27: 5 residues within 4Å: Chain F: D.104, D.108, E.257 Ligands: CO.28, 210.29 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.104, F:D.108 CO.28: 6 residues within 4Å: Chain F: D.104, D.108, Q.166, E.257 Ligands: CO.27, 210.29 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.104, F:D.108, H2O.10, H2O.10 CO.30: 2 residues within 4Å: Chain F: D.73, D.77 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.77

6 x 210: PAMIDRONATE(Non-covalent)

210.4: 12 residues within 4Å: Chain A: L.101, D.104, D.108, R.113, K.191, Q.232, D.235, K.249, K.259 Ligands: CO.1, CO.2, CO.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.113, A:R.113, A:K.191, A:Q.232, A:D.235, A:K.249, A:K.259 Water bridges: A:D.104, A:S.110, A:K.191 210.9: 12 residues within 4Å: Chain B: D.104, D.108, R.113, K.191, Q.232, D.235, D.236, K.249, K.259 Ligands: CO.6, CO.7, CO.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.113, B:R.113, B:Q.232, B:Q.232, B:D.235, B:K.249, B:K.259 Water bridges: B:D.104, B:D.105, B:S.110, B:K.191 210.14: 13 residues within 4Å: Chain C: D.104, D.105, D.108, R.113, K.191, Q.232, D.235, D.236, K.249, K.259 Ligands: CO.11, CO.12, CO.13 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.113, C:R.113, C:T.192, C:Q.232, C:D.235, C:K.249, C:K.249 210.19: 12 residues within 4Å: Chain D: L.101, D.104, D.108, R.113, K.191, Q.232, D.235, K.249, K.259 Ligands: CO.16, CO.17, CO.18 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.113, D:R.113, D:K.191, D:Q.232, D:D.235, D:K.249, D:K.259 Water bridges: D:D.104, D:D.105, D:S.110, D:K.191 210.24: 12 residues within 4Å: Chain E: D.104, D.108, R.113, K.191, Q.232, D.235, D.236, K.249, K.259 Ligands: CO.21, CO.22, CO.23 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:R.113, E:R.113, E:Q.232, E:Q.232, E:D.235, E:K.249, E:K.259 Water bridges: E:D.104, E:S.110, E:K.191, E:D.236 210.29: 13 residues within 4Å: Chain F: D.104, D.105, D.108, R.113, K.191, Q.232, D.235, D.236, K.249, K.259 Ligands: CO.26, CO.27, CO.28 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.113, F:R.113, F:T.192, F:Q.232, F:D.235, F:K.249, F:K.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, M. et al., Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase. Acs Chem.Biol. (2016)

Release Date

2016-01-20

Peptides

Fusicoccadiene synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Fusicoccadiene synthase

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