SMTL ID : 2wlu.1

Iron-bound crystal structure of Streptococcus pyogenes Dpr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-12-mer

Ligands

12 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Ligands: NA.6, NA.11 8 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 4 interactions with chain A Water bridges: C:N.148, C:N.148, C:D.149, B:N.148, A:N.148, A:N.148, A:D.149, A:D.149 NA.6: 2 residues within 4Å: Ligands: NA.1, NA.11 11 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B, 2 interactions with chain A Water bridges: C:N.148, C:N.148, C:N.148, C:D.149, C:D.149, B:N.148, B:N.148, B:N.148, B:D.149, A:D.149, A:D.149 NA.11: 2 residues within 4Å: Ligands: NA.1, NA.6 10 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A, 1 interactions with chain B Water bridges: C:N.148, C:N.148, C:N.148, C:D.149, A:N.148, A:N.148, A:N.148, A:D.149, A:D.149, B:D.149 NA.16: 2 residues within 4Å: Ligands: NA.31, NA.41 10 PLIP interactions: 5 interactions with chain G, 3 interactions with chain D, 2 interactions with chain I Water bridges: G:N.148, G:N.148, G:D.149, G:D.149, G:D.149, D:N.148, D:D.149, D:D.149, I:N.148, I:D.149 NA.21: 2 residues within 4Å: Ligands: NA.26, NA.36 11 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E, 3 interactions with chain H Water bridges: F:N.148, F:N.148, F:N.148, F:D.149, F:D.149, E:N.148, E:D.149, E:D.149, H:N.148, H:D.149, H:D.149 NA.26: 2 residues within 4Å: Ligands: NA.21, NA.36 10 PLIP interactions: 2 interactions with chain F, 6 interactions with chain E, 2 interactions with chain H Water bridges: F:N.148, F:D.149, E:N.148, E:N.148, E:D.149, E:D.149, E:D.149, E:D.149, H:N.148, H:N.148 NA.31: 2 residues within 4Å: Ligands: NA.16, NA.41 11 PLIP interactions: 4 interactions with chain G, 5 interactions with chain D, 2 interactions with chain I Water bridges: G:N.148, G:D.149, G:D.149, G:D.149, D:N.148, D:N.148, D:N.148, D:D.149, D:D.149, I:N.148, I:N.148 NA.36: 2 residues within 4Å: Ligands: NA.21, NA.26 10 PLIP interactions: 2 interactions with chain F, 6 interactions with chain E, 2 interactions with chain H Water bridges: F:N.148, F:D.149, E:N.148, E:N.148, E:D.149, E:D.149, E:D.149, E:D.149, H:N.148, H:N.148 NA.41: 2 residues within 4Å: Ligands: NA.16, NA.31 10 PLIP interactions: 2 interactions with chain D, 3 interactions with chain I, 5 interactions with chain G Water bridges: D:N.148, D:N.148, I:N.148, I:D.149, I:D.149, G:N.148, G:N.148, G:N.148, G:D.149, G:D.149 NA.46: 2 residues within 4Å: Ligands: NA.51, NA.56 7 PLIP interactions: 3 interactions with chain K, 4 interactions with chain L Water bridges: K:N.148, K:N.148, K:D.149, L:N.148, L:N.148, L:D.149, L:D.149 NA.51: 2 residues within 4Å: Ligands: NA.46, NA.56 10 PLIP interactions: 6 interactions with chain K, 2 interactions with chain L, 2 interactions with chain J Water bridges: K:N.148, K:N.148, K:N.148, K:D.149, K:D.149, K:D.149, L:N.148, L:D.149, J:N.148, J:D.149 NA.56: 2 residues within 4Å: Ligands: NA.46, NA.51 10 PLIP interactions: 5 interactions with chain K, 2 interactions with chain L, 3 interactions with chain J Water bridges: K:N.148, K:N.148, K:D.149, K:D.149, K:D.149, L:N.148, L:D.149, J:N.148, J:D.149, J:D.149

12 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: D.77, E.81 Chain F: H.50, H.62 Ligands: GOL.3 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: A:D.77, A:D.77, A:E.81, F:H.50, H2O.46 FE.7: 5 residues within 4Å: Chain B: D.77, E.81 Chain D: H.50, H.62 Ligands: GOL.8 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.77, B:D.77, B:E.81, D:H.50, H2O.29 FE.12: 5 residues within 4Å: Chain C: D.77, E.81 Chain J: H.50, H.62 Ligands: GOL.13 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: J:H.50, C:D.77, C:D.77, C:E.81, H2O.80 FE.17: 5 residues within 4Å: Chain B: H.50, H.62 Chain D: D.77, E.81 Ligands: GOL.18 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.50, D:D.77, D:D.77, D:E.81, H2O.12 FE.22: 5 residues within 4Å: Chain E: D.77, E.81 Chain G: H.50, H.62 Ligands: GOL.23 5 PLIP interactions: 1 interactions with chain G, 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: G:H.50, E:D.77, E:D.77, E:E.81, H2O.54 FE.27: 5 residues within 4Å: Chain A: H.50, H.62 Chain F: D.77, E.81 Ligands: GOL.28 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: F:D.77, F:D.77, F:E.81, A:H.50, H2O.3 FE.32: 5 residues within 4Å: Chain E: H.50, H.62 Chain G: D.77, E.81 Ligands: GOL.33 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: G:D.77, G:D.77, G:E.81, E:H.50, H2O.37 FE.37: 5 residues within 4Å: Chain H: D.77, E.81 Chain K: H.50, H.62 Ligands: GOL.38 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: H:D.77, H:D.77, H:E.81, K:H.50, H2O.89 FE.42: 5 residues within 4Å: Chain I: D.77, E.81 Chain L: H.50, H.62 Ligands: GOL.43 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: I:D.77, I:D.77, I:E.81, L:H.50, H2O.97 FE.47: 5 residues within 4Å: Chain C: H.50, H.62 Chain J: D.77, E.81 Ligands: GOL.48 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: J:D.77, J:D.77, J:E.81, C:H.50, H2O.20 FE.52: 5 residues within 4Å: Chain H: H.50, H.62 Chain K: D.77, E.81 Ligands: GOL.53 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: K:D.77, K:D.77, K:E.81, H:H.50, H2O.63 FE.57: 5 residues within 4Å: Chain I: H.50, H.62 Chain L: D.77, E.81 Ligands: GOL.58 5 PLIP interactions: 1 interactions with chain I, 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: I:H.50, L:D.77, L:D.77, L:E.81, H2O.72

36 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: D.77, E.81 Chain C: K.160 Chain F: H.50, H.62, D.66 Ligands: FE.2 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: K.155, E.159 Chain B: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: K.160 Chain B: D.77, E.81 Chain D: H.50, H.62, D.66 Ligands: FE.7 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain B: K.155, E.159 Chain C: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain B: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: K.160 Chain C: D.77, E.81 Chain J: H.50, H.62, D.66 Ligands: FE.12 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: N.25, R.82, I.86, G.143, D.144 Chain C: K.155, E.159 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain C: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: H.50, H.62, D.66 Chain D: D.77, E.81 Chain I: K.160 Ligands: FE.17 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain D: K.155, E.159 Chain G: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain D: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain E: D.77, E.81 Chain G: H.50, H.62, D.66 Chain H: K.160 Ligands: FE.22 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain E: K.155, E.159 Chain F: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain E: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain A: H.50, H.62, D.66 Chain E: K.160 Chain F: D.77, E.81 Ligands: FE.27 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain F: K.155, E.159 Chain H: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain F: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain D: K.160 Chain E: H.50, H.62, D.66 Chain G: D.77, E.81 Ligands: FE.32 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain G: K.155, E.159 Chain I: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain G: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain F: K.160 Chain H: D.77, E.81 Chain K: H.50, H.62, D.66 Ligands: FE.37 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain E: N.25, R.82, I.86, G.143, D.144 Chain H: K.155, E.159 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain H: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain G: K.160 Chain I: D.77, E.81 Chain L: H.50, H.62, D.66 Ligands: FE.42 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain D: N.25, R.82, I.86, G.143, D.144 Chain I: K.155, E.159 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain I: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain C: H.50, H.62, D.66 Chain J: D.77, E.81 Chain K: K.160 Ligands: FE.47 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain J: K.155, E.159 Chain L: N.25, R.82, I.86, G.143, D.144 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain J: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain H: H.50, H.62, D.66 Chain K: D.77, E.81 Chain L: K.160 Ligands: FE.52 Ligand excluded by PLIP GOL.54: 7 residues within 4Å: Chain J: N.25, R.82, I.86, G.143, D.144 Chain K: K.155, E.159 Ligand excluded by PLIP GOL.55: 4 residues within 4Å: Chain K: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain I: H.50, H.62, D.66 Chain J: K.160 Chain L: D.77, E.81 Ligands: FE.57 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain K: N.25, R.82, I.86, G.143, D.144 Chain L: K.155, E.159 Ligand excluded by PLIP GOL.60: 4 residues within 4Å: Chain L: A.115, A.119, R.169, Q.171 Ligand excluded by PLIP

Links

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Citation

Haikarainen, T. et al., Crystal Structures of Streptococcus Pyogenes Dpr Reveal a Dodecameric Iron-Binding Protein with a Ferroxidase Site. J.Biol.Inorg.Chem. (2010)

Release Date

2009-09-15

Peptides

DPS-LIKE 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

DPS-LIKE PEROXIDE RESISTANCE PROTEIN

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