SMTL ID : 2ahr.1 (3 other biounits)

Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase from Human Pathogen Streptococcus pyogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 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: 5 residues within 4Å: Chain C: G.92, R.97, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.97, C:A.256, C:L.259 NA.10: 5 residues within 4Å: Chain D: G.92, R.97, A.256, K.257, L.259 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.97, D:K.257, D:L.259 Water bridges: D:S.94 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: 5 residues within 4Å: Chain H: G.92, R.97, A.256, K.257, L.259 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.92, H:R.97 NA.25: 5 residues within 4Å: Chain I: G.92, R.97, A.256, K.257, L.259 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:R.97, I:A.256 Water bridges: I:S.94 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

10 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 24 residues within 4Å: Chain A: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113, M.115 Chain D: A.221, I.222, S.224 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:V.11, A:K.13, A:S.34, A:I.68, A:A.91, D:A.221, D:S.224 Water bridges: A:V.11, A:V.11, A:G.12, A:A.15, A:S.34, A:R.38, D:S.224 Salt bridges: A:R.38 NAP.5: 22 residues within 4Å: Chain B: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113 Chain C: I.222, S.224 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.13, B:S.34, B:S.34, B:I.68, B:A.91, C:A.221 Water bridges: B:V.11, B:G.12, B:A.15, B:S.34 Salt bridges: B:R.38 NAP.8: 24 residues within 4Å: Chain B: A.221, I.222, S.224, P.225 Chain C: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, V.76, M.89, A.90, A.91, M.112, P.113, M.115 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.13, C:S.34, C:I.68, C:A.91, B:A.221, B:S.224 Water bridges: C:V.11, C:A.15, C:A.15, C:S.34, C:S.34, C:K.69 Salt bridges: C:R.38 NAP.11: 24 residues within 4Å: Chain A: A.221, I.222, S.224 Chain D: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113, M.115 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:K.13, D:S.34, D:S.34, D:I.68, D:A.91, A:A.221, A:S.224 Water bridges: D:V.11, D:V.11, D:G.12, D:K.13, D:K.13, D:A.15, D:H.54 Salt bridges: D:R.38 NAP.14: 24 residues within 4Å: Chain E: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113, M.115 Chain J: A.221, I.222, S.224 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain J Hydrogen bonds: E:K.13, E:S.34, E:I.68, E:A.91, J:A.221, J:S.224 Water bridges: E:G.12, E:A.15, E:S.34, E:S.34, E:S.34, E:A.91, J:S.224 Salt bridges: E:R.38 NAP.17: 24 residues within 4Å: Chain F: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113, M.115 Chain I: A.221, I.222, S.224 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain I Hydrogen bonds: F:V.11, F:K.13, F:S.34, F:I.68, F:A.91, I:A.221, I:S.224 Water bridges: F:V.11, F:V.11, F:G.12, F:A.15, F:S.34, F:R.38, I:S.224 Salt bridges: F:R.38 NAP.20: 22 residues within 4Å: Chain G: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113 Chain H: I.222, S.224 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:K.13, G:S.34, G:S.34, G:I.68, G:A.91, H:A.221 Water bridges: G:V.11, G:G.12, G:A.15, G:S.34 Salt bridges: G:R.38 NAP.23: 24 residues within 4Å: Chain G: A.221, I.222, S.224, P.225 Chain H: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, V.76, M.89, A.90, A.91, M.112, P.113, M.115 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:K.13, H:S.34, H:I.68, H:A.91, G:A.221, G:S.224 Water bridges: H:V.11, H:A.15, H:A.15, H:S.34, H:S.34, H:K.69 Salt bridges: H:R.38 NAP.26: 24 residues within 4Å: Chain F: A.221, I.222, S.224 Chain I: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113, M.115 15 PLIP interactions: 13 interactions with chain I, 2 interactions with chain F Hydrogen bonds: I:K.13, I:S.34, I:S.34, I:I.68, I:A.91, F:A.221, F:S.224 Water bridges: I:V.11, I:V.11, I:G.12, I:K.13, I:K.13, I:A.15, I:H.54 Salt bridges: I:R.38 NAP.29: 24 residues within 4Å: Chain E: A.221, I.222, S.224 Chain J: G.10, V.11, G.12, K.13, M.14, G.33, S.34, R.38, H.54, G.67, I.68, K.69, P.70, L.72, V.76, M.89, A.90, A.91, M.112, P.113, M.115 14 PLIP interactions: 11 interactions with chain J, 3 interactions with chain E Hydrogen bonds: J:K.13, J:S.34, J:I.68, J:A.91, E:A.221, E:S.224 Water bridges: J:G.12, J:A.15, J:S.34, J:S.34, J:S.34, J:A.91, E:S.224 Salt bridges: J:R.38

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: D.250, I.253, D.254, K.257 Chain D: N.186 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.186 FMT.6: 5 residues within 4Å: Chain B: D.250, I.253, D.254, K.257 Chain C: N.186 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Water bridges: C:N.186, B:D.250, B:D.250, B:D.254 FMT.9: 5 residues within 4Å: Chain B: N.186 Chain C: D.250, I.253, D.254, K.257 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.185, B:K.185 FMT.12: 5 residues within 4Å: Chain A: N.186 Chain D: D.250, I.253, D.254, K.257 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.257 Water bridges: A:N.186 FMT.15: 4 residues within 4Å: Chain E: I.253, D.254, K.257 Chain J: N.186 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E Water bridges: J:K.185 Hydrogen bonds: E:K.257 FMT.18: 5 residues within 4Å: Chain F: D.250, I.253, D.254, K.257 Chain I: N.186 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.186 FMT.21: 5 residues within 4Å: Chain G: D.250, I.253, D.254, K.257 Chain H: N.186 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Water bridges: G:D.250, G:D.250, G:D.254, H:N.186 FMT.24: 5 residues within 4Å: Chain G: N.186 Chain H: D.250, I.253, D.254, K.257 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:D.254 Water bridges: G:K.185, G:K.185 FMT.27: 5 residues within 4Å: Chain F: N.186 Chain I: D.250, I.253, D.254, K.257 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain F Hydrogen bonds: I:K.257 Water bridges: F:N.186 FMT.30: 4 residues within 4Å: Chain E: N.186 Chain J: I.253, D.254, K.257 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain E Hydrogen bonds: J:D.254, J:K.257 Water bridges: E:K.185

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

2005-09-13

Peptides

putative pyrroline 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

putative pyrroline carboxylate reductase

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