SMTL ID : 2xgw.1

ZINC-BOUND CRYSTAL STRUCTURE OF STREPTOCOCCUS PYOGENES DPR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-12-mer

Ligands

36 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.93, E.97 Chain G: H.66, D.82 Ligands: ZN.2 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: A:D.93, G:H.66, G:D.82, H2O.7 ZN.2: 5 residues within 4Å: Chain A: E.97 Chain G: H.66, H.78 Ligands: ZN.1, SIN.5 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: A:E.97, A:E.97, G:H.78, H2O.7 ZN.3: 4 residues within 4Å: Chain A: K.115, H.116 Chain G: K.123 Ligands: CL.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.116, H2O.8, H2O.8 ZN.7: 5 residues within 4Å: Chain B: D.93, E.97 Chain F: H.66, D.82 Ligands: ZN.8 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:H.66, F:D.82, B:D.93, H2O.15 ZN.8: 5 residues within 4Å: Chain B: E.97 Chain F: H.66, H.78 Ligands: ZN.7, SIN.11 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:E.97, B:E.97, F:H.78, H2O.15 ZN.9: 4 residues within 4Å: Chain B: K.115, H.116 Chain F: K.123 Ligands: CL.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.116, H2O.15, H2O.15 ZN.13: 5 residues within 4Å: Chain C: D.93, E.97 Chain L: H.66, D.82 Ligands: ZN.14 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: L:H.66, L:D.82, C:D.93, H2O.22 ZN.14: 5 residues within 4Å: Chain C: E.97 Chain L: H.66, H.78 Ligands: ZN.13, SIN.17 4 PLIP interactions: 1 interactions with chain L, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: L:H.78, C:E.97, C:E.97, H2O.22 ZN.15: 4 residues within 4Å: Chain C: K.115, H.116 Chain L: K.123 Ligands: CL.16 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.116, H2O.22, H2O.22 ZN.19: 5 residues within 4Å: Chain D: D.93, E.97 Chain H: H.66, D.82 Ligands: ZN.20 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: D:D.93, H:H.66, H:D.82, H2O.29 ZN.20: 5 residues within 4Å: Chain D: E.97 Chain H: H.66, H.78 Ligands: ZN.19, SIN.23 4 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: H:H.78, D:E.97, D:E.97, H2O.29 ZN.21: 4 residues within 4Å: Chain D: K.115, H.116 Chain H: K.123 Ligands: CL.22 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.116, H2O.29, H2O.29 ZN.25: 5 residues within 4Å: Chain E: D.93, E.97 Chain I: H.66, D.82 Ligands: ZN.26 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: E:D.93, I:H.66, I:D.82, H2O.37 ZN.26: 5 residues within 4Å: Chain E: E.97 Chain I: H.66, H.78 Ligands: ZN.25, SIN.29 4 PLIP interactions: 1 interactions with chain I, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: I:H.78, E:E.97, E:E.97, H2O.37 ZN.27: 4 residues within 4Å: Chain E: K.115, H.116 Chain I: K.123 Ligands: CL.28 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.116, H2O.37, H2O.37 ZN.31: 5 residues within 4Å: Chain B: H.66, D.82 Chain F: D.93, E.97 Ligands: ZN.32 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.66, B:D.82, F:D.93, H2O.44 ZN.32: 5 residues within 4Å: Chain B: H.66, H.78 Chain F: E.97 Ligands: ZN.31, SIN.35 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.78, F:E.97, F:E.97, H2O.44 ZN.33: 4 residues within 4Å: Chain B: K.123 Chain F: K.115, H.116 Ligands: CL.34 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.116, H2O.44, H2O.44 ZN.37: 5 residues within 4Å: Chain A: H.66, D.82 Chain G: D.93, E.97 Ligands: ZN.38 4 PLIP interactions: 1 interactions with chain G, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: G:D.93, A:H.66, A:D.82, H2O.51 ZN.38: 5 residues within 4Å: Chain A: H.66, H.78 Chain G: E.97 Ligands: ZN.37, SIN.41 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: G:E.97, G:E.97, A:H.78, H2O.51 ZN.39: 4 residues within 4Å: Chain A: K.123 Chain G: K.115, H.116 Ligands: CL.40 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.116, H2O.51, H2O.51 ZN.43: 5 residues within 4Å: Chain D: H.66, D.82 Chain H: D.93, E.97 Ligands: ZN.44 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: D:H.66, D:D.82, H:D.93, H2O.58 ZN.44: 5 residues within 4Å: Chain D: H.66, H.78 Chain H: E.97 Ligands: ZN.43, SIN.47 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: D:H.78, H:E.97, H:E.97, H2O.58 ZN.45: 4 residues within 4Å: Chain D: K.123 Chain H: K.115, H.116 Ligands: CL.46 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.116, H2O.58, H2O.58 ZN.49: 5 residues within 4Å: Chain E: H.66, D.82 Chain I: D.93, E.97 Ligands: ZN.50 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: E:H.66, E:D.82, I:D.93, H2O.66 ZN.50: 5 residues within 4Å: Chain E: H.66, H.78 Chain I: E.97 Ligands: ZN.49, SIN.53 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: I:E.97, I:E.97, E:H.78, H2O.66 ZN.51: 4 residues within 4Å: Chain E: K.123 Chain I: K.115, H.116 Ligands: CL.52 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.116, H2O.66, H2O.66 ZN.55: 5 residues within 4Å: Chain J: D.93, E.97 Chain K: H.66, D.82 Ligands: ZN.56 4 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: K:H.66, K:D.82, J:D.93, H2O.73 ZN.56: 5 residues within 4Å: Chain J: E.97 Chain K: H.66, H.78 Ligands: ZN.55, SIN.59 4 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: K:H.78, J:E.97, J:E.97, H2O.73 ZN.57: 4 residues within 4Å: Chain J: K.115, H.116 Chain K: K.123 Ligands: CL.58 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:H.116, H2O.73, H2O.73 ZN.61: 5 residues within 4Å: Chain J: H.66, D.82 Chain K: D.93, E.97 Ligands: ZN.62 4 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: K:D.93, J:H.66, J:D.82, H2O.80 ZN.62: 5 residues within 4Å: Chain J: H.66, H.78 Chain K: E.97 Ligands: ZN.61, SIN.65 4 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: K:E.97, K:E.97, J:H.78, H2O.80 ZN.63: 4 residues within 4Å: Chain J: K.123 Chain K: K.115, H.116 Ligands: CL.64 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:H.116, H2O.80, H2O.80 ZN.67: 5 residues within 4Å: Chain C: H.66, D.82 Chain L: D.93, E.97 Ligands: ZN.68 4 PLIP interactions: 1 interactions with chain L, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: L:D.93, C:H.66, C:D.82, H2O.87 ZN.68: 5 residues within 4Å: Chain C: H.66, H.78 Chain L: E.97 Ligands: ZN.67, SIN.71 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: L:E.97, L:E.97, C:H.78, H2O.87 ZN.69: 4 residues within 4Å: Chain C: K.123 Chain L: K.115, H.116 Ligands: CL.70 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:H.116, H2O.87, H2O.88

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

CL.4: 5 residues within 4Å: Chain A: E.112, K.115, H.116 Chain G: K.123 Ligands: ZN.3 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: E.112, K.115, H.116 Chain F: K.123 Ligands: ZN.9 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: E.112, K.115, H.116 Chain L: K.123 Ligands: ZN.15 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain D: E.112, K.115, H.116 Chain H: K.123 Ligands: ZN.21 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain E: E.112, K.115, H.116 Chain I: K.123 Ligands: ZN.27 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain B: K.123 Chain F: E.112, K.115, H.116 Ligands: ZN.33 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain A: K.123 Chain G: E.112, K.115, H.116 Ligands: ZN.39 Ligand excluded by PLIP CL.46: 5 residues within 4Å: Chain D: K.123 Chain H: E.112, K.115, H.116 Ligands: ZN.45 Ligand excluded by PLIP CL.52: 5 residues within 4Å: Chain E: K.123 Chain I: E.112, K.115, H.116 Ligands: ZN.51 Ligand excluded by PLIP CL.58: 5 residues within 4Å: Chain J: E.112, K.115, H.116 Chain K: K.123 Ligands: ZN.57 Ligand excluded by PLIP CL.64: 5 residues within 4Å: Chain J: K.123 Chain K: E.112, K.115, H.116 Ligands: ZN.63 Ligand excluded by PLIP CL.70: 5 residues within 4Å: Chain C: K.123 Chain L: E.112, K.115, H.116 Ligands: ZN.69 Ligand excluded by PLIP

12 x SIN: SUCCINIC ACID(Non-covalent)

SIN.5: 5 residues within 4Å: Chain A: E.97 Chain C: K.176, M.180 Chain G: H.78 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain G Water bridges: C:K.176, C:K.176 Salt bridges: C:K.176, C:K.176, G:H.78 SIN.11: 5 residues within 4Å: Chain B: E.97 Chain F: H.78 Chain J: K.176, M.180 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain F Water bridges: J:K.176, J:K.176 Salt bridges: J:K.176, J:K.176, F:H.78 SIN.17: 5 residues within 4Å: Chain C: E.97 Chain D: K.176, M.180 Chain L: H.78 Ligands: ZN.14 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C, 1 interactions with chain L Water bridges: D:K.176, C:D.93 Salt bridges: D:K.176, D:K.176, L:H.78 Hydrogen bonds: C:E.97 SIN.23: 5 residues within 4Å: Chain A: K.176, M.180 Chain D: E.97 Chain H: H.78 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain H Water bridges: A:K.176, A:K.176 Salt bridges: A:K.176, A:K.176, H:H.78 SIN.29: 5 residues within 4Å: Chain E: E.97 Chain F: K.176, M.180 Chain I: H.78 Ligands: ZN.26 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain I Water bridges: F:K.176, F:K.176 Salt bridges: F:K.176, F:K.176, I:H.78 SIN.35: 5 residues within 4Å: Chain B: H.78 Chain F: E.97 Chain G: K.176, M.180 Ligands: ZN.32 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain G Salt bridges: B:H.78, G:K.176, G:K.176 Water bridges: G:K.176, G:K.176 SIN.41: 5 residues within 4Å: Chain A: H.78 Chain E: K.176, M.180 Chain G: E.97 Ligands: ZN.38 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Water bridges: E:K.176, E:K.176 Salt bridges: E:K.176, E:K.176, A:H.78 SIN.47: 5 residues within 4Å: Chain D: H.78 Chain H: E.97 Chain K: K.176, M.180 Ligands: ZN.44 6 PLIP interactions: 2 interactions with chain H, 1 interactions with chain D, 3 interactions with chain K Hydrogen bonds: H:E.97 Water bridges: H:D.93, K:K.176 Salt bridges: D:H.78, K:K.176, K:K.176 SIN.53: 5 residues within 4Å: Chain E: H.78 Chain H: K.176, M.180 Chain I: E.97 Ligands: ZN.50 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain E Water bridges: H:K.176, H:K.176 Salt bridges: H:K.176, H:K.176, E:H.78 SIN.59: 5 residues within 4Å: Chain J: E.97 Chain K: H.78 Chain L: K.176, M.180 Ligands: ZN.56 5 PLIP interactions: 1 interactions with chain K, 4 interactions with chain L Salt bridges: K:H.78, L:K.176, L:K.176 Water bridges: L:K.176, L:K.176 SIN.65: 5 residues within 4Å: Chain I: K.176, M.180 Chain J: H.78 Chain K: E.97 Ligands: ZN.62 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain J Water bridges: I:K.176, I:K.176 Salt bridges: I:K.176, I:K.176, J:H.78 SIN.71: 5 residues within 4Å: Chain B: K.176, M.180 Chain C: H.78 Chain L: E.97 Ligands: ZN.68 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Water bridges: B:K.176, B:K.176 Salt bridges: B:K.176, B:K.176, C:H.78

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.171, E.175 Chain D: N.41, R.98, I.102, G.159, D.160 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.41, D:R.98, A:E.175 Water bridges: D:R.98, D:A.161, A:Q.149 GOL.12: 7 residues within 4Å: Chain B: K.171, E.175 Chain L: N.41, R.98, I.102, G.159, D.160 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain L Hydrogen bonds: B:E.175, L:N.41, L:R.98 Water bridges: B:Q.149, L:R.98, L:A.161 GOL.18: 7 residues within 4Å: Chain A: N.41, R.98, I.102, G.159, D.160 Chain C: K.171, E.175 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.41, A:R.98, C:E.175 Water bridges: A:R.98, A:A.161, C:Q.149 GOL.24: 7 residues within 4Å: Chain C: N.41, R.98, I.102, G.159, D.160 Chain D: K.171, E.175 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.41, C:R.98, D:E.175 Water bridges: C:R.98, C:A.161, D:Q.149 GOL.30: 7 residues within 4Å: Chain E: K.171, E.175 Chain G: N.41, R.98, I.102, G.159, D.160 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain G Hydrogen bonds: E:E.175, G:N.41, G:R.98 Water bridges: E:Q.149, G:R.98, G:A.161 GOL.36: 7 residues within 4Å: Chain E: N.41, R.98, I.102, G.159, D.160 Chain F: K.171, E.175 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.41, E:R.98, F:E.175 Water bridges: E:R.98, E:A.161, F:Q.149 GOL.42: 7 residues within 4Å: Chain F: N.41, R.98, I.102, G.159, D.160 Chain G: K.171, E.175 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:N.41, F:R.98, G:E.175 Water bridges: F:R.98, F:A.161, G:Q.149 GOL.48: 7 residues within 4Å: Chain H: K.171, E.175 Chain I: N.41, R.98, I.102, G.159, D.160 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:N.41, I:R.98, H:E.175 Water bridges: I:R.98, I:A.161, H:Q.149 GOL.54: 7 residues within 4Å: Chain I: K.171, E.175 Chain K: N.41, R.98, I.102, G.159, D.160 6 PLIP interactions: 4 interactions with chain K, 2 interactions with chain I Hydrogen bonds: K:N.41, K:R.98, I:E.175 Water bridges: K:R.98, K:A.161, I:Q.149 GOL.60: 7 residues within 4Å: Chain B: N.41, R.98, I.102, G.159, D.160 Chain J: K.171, E.175 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain J Hydrogen bonds: B:N.41, B:R.98, J:E.175 Water bridges: B:R.98, B:A.161, J:Q.149 GOL.66: 7 residues within 4Å: Chain H: N.41, R.98, I.102, G.159, D.160 Chain K: K.171, E.175 6 PLIP interactions: 2 interactions with chain K, 4 interactions with chain H Hydrogen bonds: K:E.175, H:N.41, H:R.98 Water bridges: K:Q.149, H:R.98, H:A.161 GOL.72: 7 residues within 4Å: Chain J: N.41, R.98, I.102, G.159, D.160 Chain L: K.171, E.175 6 PLIP interactions: 2 interactions with chain L, 4 interactions with chain J Hydrogen bonds: L:E.175, J:N.41, J:R.98 Water bridges: L:Q.149, J:R.98, J:A.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haikarainen, T. et al., Structural Characterization and Biological Implications of Di-Zinc Binding in the Ferroxidase Center of Streptococcus Pyogenes Dpr. Biochem.Biophys.Res.Commun. (2010)

Release Date

2010-08-11

Peptides

PEROXIDE RESISTANCE PROTEIN: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

PEROXIDE RESISTANCE PROTEIN