SMTL ID : 4tm7.1

Crystal structure of 6-phosphogluconolactonase from Mycobacterium smegmatis N131D mutant soaked with CuSO4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: Q.48, H.79, Y.81, D.143, S.146, S.147 Ligands: CU1.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.48, A:Q.48, A:Y.81, A:S.146, A:S.147 EDO.2: 5 residues within 4Å: Chain A: A.117, A.119, G.135, Y.136 Ligands: CU.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.119 Water bridges: A:Y.136 EDO.3: 8 residues within 4Å: Chain A: A.38, S.41, A.42, R.46, D.152, V.153, E.207, E.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.38, A:E.207, A:E.242 Water bridges: A:R.46, A:R.46

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: R.86, H.163, F.168, K.189, R.194 Ligands: CU.11 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.86, A:R.194 Salt bridges: A:R.86, A:H.163, A:K.189, A:R.194

1 x CU1: COPPER (I) ION(Non-covalent)

CU1.5: 5 residues within 4Å: Chain A: H.79, V.113, N.114, H.116 Ligands: EDO.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.79, A:H.116, H2O.2

15 x CU: COPPER (II) ION(Non-covalent)

CU.6: 1 residues within 4Å: Chain A: H.21 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.21, H2O.1 CU.7: 1 residues within 4Å: Chain A: H.107 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.107, H2O.2 CU.8: 3 residues within 4Å: Chain A: D.33, D.37, R.69 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.37, H2O.5, H2O.7 CU.9: 2 residues within 4Å: Chain A: D.128 Ligands: CU.18 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.128, H2O.2 CU.10: 2 residues within 4Å: Chain A: D.219, K.255 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.219, H2O.7 CU.11: 4 residues within 4Å: Chain A: H.163, N.165, R.194 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.163, A:N.165 CU.12: 1 residues within 4Å: Chain A: D.172 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.172, A:D.172, H2O.6 CU.13: 2 residues within 4Å: Chain A: E.124 Ligands: EDO.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.124, H2O.3 CU.14: 1 residues within 4Å: Chain A: E.250 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.250, H2O.7 CU.15: 1 residues within 4Å: Chain A: D.23 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.23, H2O.2, H2O.2, H2O.6 CU.16: 2 residues within 4Å: Chain A: E.94 Ligands: CU.19 No protein-ligand interaction detected (PLIP) CU.17: 1 residues within 4Å: Chain A: D.91 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.91, H2O.7 CU.18: 4 residues within 4Å: Chain A: D.128, E.130 Ligands: CU.9, CL.21 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.128, H2O.2, H2O.6 CU.19: 3 residues within 4Å: Chain A: D.92, E.94 Ligands: CU.16 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.92 CU.20: 1 residues within 4Å: Chain A: E.102 No protein-ligand interaction detected (PLIP)

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

CL.21: 1 residues within 4Å: Ligands: CU.18 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain A: D.93 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujieda, N. et al., Enzyme repurposing of a hydrolase as an emergent peroxidase upon metal binding. Chem Sci (2015)

Release Date

2015-06-03

Peptides

6-phosphogluconolactonase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

6-phosphogluconolactonase

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