SMTL ID : 4hpn.1

Crystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

16 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.194, A:E.220, H2O.1, H2O.5, H2O.5 CA.2: 2 residues within 4Å: Chain A: D.209, G.237 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.237, H2O.4, H2O.6, H2O.7, H2O.8 CA.5: 3 residues within 4Å: Chain B: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.194, B:E.220, H2O.20, H2O.23, H2O.24 CA.6: 2 residues within 4Å: Chain B: D.209, G.237 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.237, H2O.22, H2O.24, H2O.26, H2O.26 CA.9: 3 residues within 4Å: Chain C: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.194, C:E.220, H2O.38, H2O.41, H2O.42 CA.10: 2 residues within 4Å: Chain C: D.209, G.237 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:G.237, H2O.41, H2O.43, H2O.44, H2O.45 CA.13: 3 residues within 4Å: Chain D: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.194, D:E.220, H2O.56, H2O.60, H2O.61 CA.14: 2 residues within 4Å: Chain D: D.209, G.237 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:G.237, H2O.59, H2O.61, H2O.62, H2O.63 CA.17: 3 residues within 4Å: Chain E: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.194, E:E.220, H2O.75, H2O.78, H2O.79 CA.18: 2 residues within 4Å: Chain E: D.209, G.237 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:G.237, H2O.77, H2O.80, H2O.81, H2O.82 CA.21: 3 residues within 4Å: Chain F: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.194, F:E.220, H2O.93, H2O.97, H2O.98 CA.22: 2 residues within 4Å: Chain F: D.209, G.237 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:G.237, H2O.96, H2O.98, H2O.99, H2O.100 CA.25: 3 residues within 4Å: Chain G: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.194, G:E.220, H2O.112, H2O.115, H2O.116 CA.26: 2 residues within 4Å: Chain G: D.209, G.237 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:G.237, H2O.114, H2O.116, H2O.118, H2O.118 CA.29: 3 residues within 4Å: Chain H: D.194, E.220, E.246 5 PLIP interactions: 2 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.194, H:E.220, H2O.130, H2O.134, H2O.134 CA.30: 2 residues within 4Å: Chain H: D.209, G.237 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:G.237, H2O.133, H2O.135, H2O.136, H2O.137

8 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 5 residues within 4Å: Chain A: H.13, R.14, D.16, H.334 Ligands: NI.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.16 IMD.7: 5 residues within 4Å: Chain B: H.13, R.14, D.16, H.334 Ligands: NI.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.16 IMD.11: 5 residues within 4Å: Chain C: H.13, R.14, D.16, H.334 Ligands: NI.12 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.16 IMD.15: 5 residues within 4Å: Chain D: H.13, R.14, D.16, H.334 Ligands: NI.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.13 Water bridges: D:D.16 IMD.19: 5 residues within 4Å: Chain E: H.13, R.14, D.16, H.334 Ligands: NI.20 1 PLIP interactions: 1 interactions with chain E Water bridges: E:D.16 IMD.23: 5 residues within 4Å: Chain F: H.13, R.14, D.16, H.334 Ligands: NI.24 1 PLIP interactions: 1 interactions with chain F Water bridges: F:D.16 IMD.27: 5 residues within 4Å: Chain G: H.13, R.14, D.16, H.334 Ligands: NI.28 1 PLIP interactions: 1 interactions with chain G Water bridges: G:D.16 IMD.31: 5 residues within 4Å: Chain H: H.13, R.14, D.16, H.334 Ligands: NI.32 1 PLIP interactions: 1 interactions with chain H Water bridges: H:D.16

8 x NI: NICKEL (II) ION(Non-covalent)

NI.4: 3 residues within 4Å: Chain A: H.13, H.334 Ligands: IMD.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.13, A:H.334 NI.8: 3 residues within 4Å: Chain B: H.13, H.334 Ligands: IMD.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.13, B:H.334 NI.12: 3 residues within 4Å: Chain C: H.13, H.334 Ligands: IMD.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.13, C:H.334 NI.16: 3 residues within 4Å: Chain D: H.13, H.334 Ligands: IMD.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.13, D:H.334 NI.20: 3 residues within 4Å: Chain E: H.13, H.334 Ligands: IMD.19 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.13, E:H.334 NI.24: 3 residues within 4Å: Chain F: H.13, H.334 Ligands: IMD.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.13, F:H.334 NI.28: 3 residues within 4Å: Chain G: H.13, H.334 Ligands: IMD.27 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.13, G:H.334 NI.32: 3 residues within 4Å: Chain H: H.13, H.334 Ligands: IMD.31 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.13, H:H.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation. Acta Crystallogr F Struct Biol Commun (2016)

Release Date

2012-11-07

Peptides

Putative uncharacterized protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Putative uncharacterized protein

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