SMTL ID : 2amf.1

Crystal structure of 1-Pyrroline-5-Carboxylate Reductase from Human Pathogen Streptococcus Pyogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-10-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: G.92, R.97, A.256, K.257, L.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:K.257 NA.4: 5 residues within 4Å: Chain B: G.92, R.97, A.256, K.257, L.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.97, B:L.259 NA.7: 4 residues within 4Å: Chain C: G.92, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.97, C:L.259, C:L.259 NA.10: 5 residues within 4Å: Chain D: G.92, R.97, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.97, D:K.257, D:L.259 NA.13: 5 residues within 4Å: Chain E: G.92, R.97, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.97, E:L.259, E:L.259 NA.16: 5 residues within 4Å: Chain F: G.92, R.97, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.92, F:R.97, F:L.259 NA.19: 5 residues within 4Å: Chain G: G.92, R.97, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.97, G:A.256, G:L.259 NA.22: 4 residues within 4Å: Chain H: G.92, A.256, K.257, L.259 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.97, H:K.257 NA.25: 5 residues within 4Å: Chain I: G.92, R.97, A.256, K.257, L.259 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.97, I:L.259 NA.28: 5 residues within 4Å: Chain J: G.92, R.97, A.256, K.257, L.259 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.97, J:K.257

20 x PRO: PROLINE(Non-covalent)

PRO.2: 8 residues within 4Å: Chain A: I.222, S.224 Chain D: M.14, M.89, M.112, P.113, M.115 Ligands: PRO.3 5 PLIP interactions: 5 interactions with chain D, Hydrophobic interactions: D:M.14 Water bridges: D:M.89, D:M.89, D:A.91, D:M.115 PRO.3: 9 residues within 4Å: Chain A: I.222, S.224, G.227, T.228, T.229 Chain D: T.162, G.166, S.167 Ligands: PRO.2 9 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: A:S.224, A:S.224, A:T.228, A:T.229, A:T.229, A:T.229, P.3 Water bridges: A:G.227 Hydrophobic interactions: D:T.162 PRO.5: 8 residues within 4Å: Chain B: I.222, S.224 Chain C: M.14, M.89, M.112, P.113, M.115 Ligands: PRO.6 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain C Hydrogen bonds: P.5, C:P.113 Hydrophobic interactions: C:M.14 Water bridges: C:A.91, C:M.115 PRO.6: 9 residues within 4Å: Chain B: I.222, S.224, G.227, T.228, T.229 Chain C: T.162, G.166, S.167 Ligands: PRO.5 11 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: B:I.222, B:I.222, B:S.224, B:S.224, B:T.228, B:T.229, B:T.229, P.6, P.6 Water bridges: B:G.227 Hydrophobic interactions: C:T.162 PRO.8: 8 residues within 4Å: Chain B: M.14, M.89, M.112, P.113, M.115 Chain C: I.222, S.224 Ligands: PRO.9 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:M.14 Water bridges: B:M.115 PRO.9: 9 residues within 4Å: Chain B: T.162, G.166, S.167 Chain C: I.222, S.224, G.227, T.228, T.229 Ligands: PRO.8 11 PLIP interactions: 8 interactions with chain C, 2 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: C:I.222, C:I.222, C:S.224, C:S.224, C:T.228, C:T.229, C:T.229, P.9, P.9 Water bridges: C:G.227 Hydrophobic interactions: B:T.162 PRO.11: 8 residues within 4Å: Chain A: M.14, M.89, M.112, P.113, M.115 Chain D: I.222, S.224 Ligands: PRO.12 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:M.14 Water bridges: A:M.115 Hydrogen bonds: P.11, P.11 PRO.12: 9 residues within 4Å: Chain A: T.162, G.166, S.167 Chain D: I.222, S.224, G.227, T.228, T.229 Ligands: PRO.11 11 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: D:I.222, D:I.222, D:S.224, D:S.224, D:T.228, D:T.229, D:T.229, P.12, P.12 Water bridges: D:G.227 Hydrophobic interactions: A:T.162 PRO.14: 9 residues within 4Å: Chain E: M.14, M.89, M.112, P.113, M.115 Chain J: A.221, I.222, S.224 Ligands: PRO.15 3 PLIP interactions: 3 interactions with chain E Water bridges: E:M.89, E:M.89, E:M.115 PRO.15: 8 residues within 4Å: Chain E: G.166, S.167 Chain J: I.222, S.224, G.227, T.228, T.229 Ligands: PRO.14 8 PLIP interactions: 7 interactions with chain J, 1 Ligand-Ligand interactions Hydrogen bonds: J:I.222, J:S.224, J:S.224, J:T.228, J:T.229, J:T.229, P.15 Water bridges: J:G.227 PRO.17: 8 residues within 4Å: Chain F: I.222, S.224 Chain I: M.14, M.89, M.112, P.113, M.115 Ligands: PRO.18 5 PLIP interactions: 5 interactions with chain I, Hydrophobic interactions: I:M.14 Water bridges: I:M.89, I:M.89, I:A.91, I:M.115 PRO.18: 9 residues within 4Å: Chain F: I.222, S.224, G.227, T.228, T.229 Chain I: T.162, G.166, S.167 Ligands: PRO.17 9 PLIP interactions: 7 interactions with chain F, 1 interactions with chain I, 1 Ligand-Ligand interactions Hydrogen bonds: F:S.224, F:S.224, F:T.228, F:T.229, F:T.229, F:T.229, P.18 Water bridges: F:G.227 Hydrophobic interactions: I:T.162 PRO.20: 8 residues within 4Å: Chain G: I.222, S.224 Chain H: M.14, M.89, M.112, P.113, M.115 Ligands: PRO.21 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Ligand interactions Hydrophobic interactions: H:M.14 Hydrogen bonds: H:P.113, P.20 Water bridges: H:A.91, H:M.115 PRO.21: 9 residues within 4Å: Chain G: I.222, S.224, G.227, T.228, T.229 Chain H: T.162, G.166, S.167 Ligands: PRO.20 11 PLIP interactions: 8 interactions with chain G, 1 interactions with chain H, 2 Ligand-Ligand interactions Hydrogen bonds: G:I.222, G:I.222, G:S.224, G:S.224, G:T.228, G:T.229, G:T.229, P.21, P.21 Water bridges: G:G.227 Hydrophobic interactions: H:T.162 PRO.23: 8 residues within 4Å: Chain G: M.14, M.89, M.112, P.113, M.115 Chain H: I.222, S.224 Ligands: PRO.24 2 PLIP interactions: 2 interactions with chain G, Hydrophobic interactions: G:M.14 Water bridges: G:M.115 PRO.24: 9 residues within 4Å: Chain G: T.162, G.166, S.167 Chain H: I.222, S.224, G.227, T.228, T.229 Ligands: PRO.23 11 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G, 2 Ligand-Ligand interactions Hydrogen bonds: H:I.222, H:I.222, H:S.224, H:S.224, H:T.228, H:T.229, H:T.229, P.24, P.24 Water bridges: H:G.227 Hydrophobic interactions: G:T.162 PRO.26: 8 residues within 4Å: Chain F: M.14, M.89, M.112, P.113, M.115 Chain I: I.222, S.224 Ligands: PRO.27 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Ligand interactions Hydrophobic interactions: F:M.14 Water bridges: F:M.115 Hydrogen bonds: P.26, P.26 PRO.27: 9 residues within 4Å: Chain F: T.162, G.166, S.167 Chain I: I.222, S.224, G.227, T.228, T.229 Ligands: PRO.26 11 PLIP interactions: 8 interactions with chain I, 1 interactions with chain F, 2 Ligand-Ligand interactions Hydrogen bonds: I:I.222, I:I.222, I:S.224, I:S.224, I:T.228, I:T.229, I:T.229, P.27, P.27 Water bridges: I:G.227 Hydrophobic interactions: F:T.162 PRO.29: 9 residues within 4Å: Chain E: A.221, I.222, S.224 Chain J: M.14, M.89, M.112, P.113, M.115 Ligands: PRO.30 4 PLIP interactions: 4 interactions with chain J, Hydrophobic interactions: J:M.14 Water bridges: J:M.89, J:M.89, J:M.115 PRO.30: 8 residues within 4Å: Chain E: I.222, S.224, G.227, T.228, T.229 Chain J: G.166, S.167 Ligands: PRO.29 8 PLIP interactions: 7 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: E:I.222, E:S.224, E:S.224, E:T.228, E:T.229, E:T.229, P.30 Water bridges: E:G.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal Structures of Delta(1)-Pyrroline-5-carboxylate Reductase from Human Pathogens Neisseria meningitides and Streptococcus pyogenes. J.Mol.Biol. (2005)

Release Date

2005-09-27

Peptides

1-Pyrroline-5-Carboxylate reductase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

1-Pyrroline-5-Carboxylate reductase

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