SMTL ID : 4ggb.1

Crystal structure of a proposed galactarolactone cycloisomerase from agrobacterium tumefaciens, TARGET EFI-500704, WITH BOUND CA, DISORDERED LOOPS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

24 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.194, A:E.220, A:E.246, H2O.3, H2O.7 CA.2: 3 residues within 4Å: Chain A: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.154, A:E.158, H2O.2, H2O.2 CA.3: 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.7, H2O.7, H2O.7, H2O.7 CA.9: 4 residues within 4Å: Chain B: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.194, B:E.220, B:E.246, H2O.10, H2O.14 CA.10: 3 residues within 4Å: Chain B: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.154, B:E.158, H2O.9, H2O.9 CA.11: 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.14, H2O.14, H2O.14, H2O.14 CA.17: 4 residues within 4Å: Chain C: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.194, C:E.220, C:E.246, H2O.17, H2O.21 CA.18: 3 residues within 4Å: Chain C: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.154, C:E.158, H2O.16, H2O.16 CA.19: 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.21, H2O.21, H2O.21, H2O.21 CA.25: 4 residues within 4Å: Chain D: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.194, D:E.220, D:E.246, H2O.24, H2O.29 CA.26: 3 residues within 4Å: Chain D: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.154, D:E.158, H2O.23, H2O.23 CA.27: 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.28, H2O.28, H2O.28, H2O.28 CA.33: 4 residues within 4Å: Chain E: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.194, E:E.220, E:E.246, H2O.31, H2O.36 CA.34: 3 residues within 4Å: Chain E: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.154, E:E.158, H2O.30, H2O.30 CA.35: 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.35, H2O.35, H2O.36, H2O.36 CA.41: 4 residues within 4Å: Chain F: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.194, F:E.220, F:E.246, H2O.38, H2O.43 CA.42: 3 residues within 4Å: Chain F: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.154, F:E.158, H2O.37, H2O.37 CA.43: 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.42, H2O.42, H2O.43, H2O.43 CA.49: 4 residues within 4Å: Chain G: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.194, G:E.220, G:E.246, H2O.46, H2O.50 CA.50: 3 residues within 4Å: Chain G: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.154, G:E.158, H2O.44, H2O.44 CA.51: 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.49, H2O.49, H2O.50, H2O.50 CA.57: 4 residues within 4Å: Chain H: D.194, E.220, E.221, E.246 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.194, H:E.220, H:E.246, H2O.53, H2O.57 CA.58: 3 residues within 4Å: Chain H: E.154, R.155, E.158 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.154, H:E.158, H2O.51, H2O.51 CA.59: 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.56, H2O.57, H2O.57, H2O.57

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

CL.4: 6 residues within 4Å: Chain A: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: V.43, W.45, R.367 Ligand excluded by PLIP CL.6: 9 residues within 4Å: Chain A: Q.90, R.91, G.92, L.93 Chain H: Q.90, R.91, G.92, L.93 Ligands: CL.62 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: A.115, S.116, M.119 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain B: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: V.43, W.45, R.367 Ligand excluded by PLIP CL.14: 9 residues within 4Å: Chain B: Q.90, R.91, G.92, L.93 Chain G: Q.90, R.91, G.92, L.93 Ligands: CL.54 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: A.115, S.116, M.119 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain C: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: V.43, W.45, R.367 Ligand excluded by PLIP CL.22: 9 residues within 4Å: Chain C: Q.90, R.91, G.92, L.93 Chain F: Q.90, R.91, G.92, L.93 Ligands: CL.46 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain C: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: A.115, S.116, M.119 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain D: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain D: V.43, W.45, R.367 Ligand excluded by PLIP CL.30: 9 residues within 4Å: Chain D: Q.90, R.91, G.92, L.93 Chain E: Q.90, R.91, G.92, L.93 Ligands: CL.38 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain D: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain D: A.115, S.116, M.119 Ligand excluded by PLIP CL.36: 6 residues within 4Å: Chain E: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain E: V.43, W.45, R.367 Ligand excluded by PLIP CL.38: 9 residues within 4Å: Chain D: Q.90, R.91, G.92, L.93 Chain E: Q.90, R.91, G.92, L.93 Ligands: CL.30 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain E: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain E: A.115, S.116, M.119 Ligand excluded by PLIP CL.44: 6 residues within 4Å: Chain F: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain F: V.43, W.45, R.367 Ligand excluded by PLIP CL.46: 9 residues within 4Å: Chain C: Q.90, R.91, G.92, L.93 Chain F: Q.90, R.91, G.92, L.93 Ligands: CL.22 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain F: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain F: A.115, S.116, M.119 Ligand excluded by PLIP CL.52: 6 residues within 4Å: Chain G: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain G: V.43, W.45, R.367 Ligand excluded by PLIP CL.54: 9 residues within 4Å: Chain B: Q.90, R.91, G.92, L.93 Chain G: Q.90, R.91, G.92, L.93 Ligands: CL.14 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain G: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain G: A.115, S.116, M.119 Ligand excluded by PLIP CL.60: 6 residues within 4Å: Chain H: R.91, H.249, G.250, R.251, Y.252, G.253 Ligand excluded by PLIP CL.61: 3 residues within 4Å: Chain H: V.43, W.45, R.367 Ligand excluded by PLIP CL.62: 9 residues within 4Å: Chain A: Q.90, R.91, G.92, L.93 Chain H: Q.90, R.91, G.92, L.93 Ligands: CL.6 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain H: I.304, D.331, N.335, R.338 Ligand excluded by PLIP CL.64: 3 residues within 4Å: Chain H: A.115, S.116, M.119 Ligand excluded by PLIP

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.,Sect.F (2016)

Release Date

2012-08-29

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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