SMTL ID : 7m3k.1

Crystal Structure of Galactonate dehydratase from Brucella melitensis biovar Abortus 2308

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: C.71, C.139, D.140 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.71, A:C.139, H2O.9, H2O.9 ZN.9: 3 residues within 4Å: Chain B: C.71, C.139, D.140 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.71, B:C.139, H2O.19, H2O.19 ZN.17: 3 residues within 4Å: Chain C: C.71, C.139, D.140 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.71, C:C.139, H2O.29, H2O.30 ZN.25: 3 residues within 4Å: Chain D: C.71, C.139, D.140 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:C.71, D:C.139, H2O.40, H2O.40

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

CL.2: 2 residues within 4Å: Chain A: R.280, H.355 Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: E.333 Ligands: CL.20 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: R.280, H.355 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: E.333 Ligands: CL.28 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: R.280, H.355 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: E.333 Ligands: CL.4 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain D: R.280, H.355 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain D: E.333 Ligands: CL.12 Ligand excluded by PLIP

8 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 5 residues within 4Å: Chain A: A.578, V.579, I.580, E.590, N.591 No protein-ligand interaction detected (PLIP) PG4.6: 7 residues within 4Å: Chain A: E.88, R.254 Chain D: R.56, R.87, E.88, G.90 Ligands: PG4.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.254 PG4.13: 5 residues within 4Å: Chain B: A.578, V.579, I.580, E.590, N.591 No protein-ligand interaction detected (PLIP) PG4.14: 7 residues within 4Å: Chain B: E.88, R.254 Chain C: R.56, R.87, E.88, G.90 Ligands: PG4.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.254 PG4.21: 5 residues within 4Å: Chain C: A.578, V.579, I.580, E.590, N.591 No protein-ligand interaction detected (PLIP) PG4.22: 7 residues within 4Å: Chain B: R.56, R.87, E.88, G.90 Chain C: E.88, R.254 Ligands: PG4.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.88, C:R.254 PG4.29: 5 residues within 4Å: Chain D: A.578, V.579, I.580, E.590, N.591 No protein-ligand interaction detected (PLIP) PG4.30: 7 residues within 4Å: Chain A: R.56, R.87, E.88, G.90 Chain D: E.88, R.254 Ligands: PG4.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.88, D:R.254

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: G.234, I.238, D.244, E.247, V.248, Y.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.247, A:Y.336 PEG.15: 6 residues within 4Å: Chain B: G.234, I.238, D.244, E.247, V.248, Y.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.247, B:Y.336 PEG.23: 6 residues within 4Å: Chain C: G.234, I.238, D.244, E.247, V.248, Y.336 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.247 PEG.31: 6 residues within 4Å: Chain D: G.234, I.238, D.244, E.247, V.248, Y.336 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.247

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 6 residues within 4Å: Chain A: R.280, K.313, Y.314, Q.351, L.353, Y.384 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.280, A:K.313, A:Q.351 Water bridges: A:Y.384 PGE.16: 6 residues within 4Å: Chain B: R.280, K.313, Y.314, Q.351, L.353, Y.384 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.280, B:K.313, B:Q.351 Water bridges: B:Y.384 PGE.24: 6 residues within 4Å: Chain C: R.280, K.313, Y.314, Q.351, L.353, Y.384 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.280, C:K.313, C:Q.351 PGE.32: 6 residues within 4Å: Chain D: R.280, K.313, Y.314, Q.351, L.353, Y.384 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.280, D:K.313, D:Q.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of Galactonate dehydratase from Brucella melitensis biovar Abortus 2308. to be published

Release Date

2021-04-07

Peptides

Galactonate dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Galactonate dehydratase