SMTL ID : 4drs.1

Crystal structure of Cryptosporidium parvum pyruvate kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: T.432, E.433, T.434, G.435, N.436, T.437 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.432, A:E.433, A:T.434, A:G.435, A:N.436, A:T.437, A:T.437, A:T.437 SO4.2: 6 residues within 4Å: Chain A: H.101, S.102, T.103, K.464, K.470, T.471 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.103, A:T.103, A:T.471, A:T.471 Water bridges: A:K.464 Salt bridges: A:K.464, A:K.470 SO4.8: 6 residues within 4Å: Chain B: I.431, T.432, E.433, T.434, N.436, T.437 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.432, B:T.432, B:E.433, B:T.434, B:G.435, B:N.436, B:T.437, B:T.437, B:T.437 SO4.9: 6 residues within 4Å: Chain B: H.101, S.102, T.103, K.464, K.470, T.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.103, B:T.471 Salt bridges: B:K.464, B:K.470 SO4.15: 6 residues within 4Å: Chain C: T.432, E.433, T.434, G.435, N.436, T.437 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.432, C:E.433, C:T.434, C:G.435, C:N.436, C:T.437, C:T.437, C:T.437 SO4.16: 6 residues within 4Å: Chain C: H.101, S.102, T.103, K.464, K.470, T.471 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.103, C:T.103, C:T.471, C:T.471 Water bridges: C:K.464 Salt bridges: C:K.464, C:K.470 SO4.22: 6 residues within 4Å: Chain D: I.431, T.432, E.433, T.434, N.436, T.437 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.432, D:T.432, D:E.433, D:T.434, D:G.435, D:N.436, D:T.437, D:T.437, D:T.437 SO4.23: 6 residues within 4Å: Chain D: H.101, S.102, T.103, K.464, K.470, T.471 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.103, D:T.471 Salt bridges: D:K.464, D:K.470

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.74, N.76, K.270, E.272, S.362 Ligands: ACT.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.74, A:N.76, A:N.76, A:K.270, A:E.272, A:S.362, A:S.362 GOL.4: 4 residues within 4Å: Chain A: N.229, P.457, E.458, R.461 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.229, A:R.461, A:R.461 GOL.10: 6 residues within 4Å: Chain B: R.74, N.76, K.270, E.272, S.362 Ligands: ACT.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.74, B:R.74, B:N.76, B:K.270, B:E.272, B:S.362, B:S.362 Water bridges: B:S.78, B:K.270 GOL.11: 4 residues within 4Å: Chain B: N.229, P.457, E.458, R.461 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.229, B:N.229, B:E.458, B:R.461 GOL.17: 6 residues within 4Å: Chain C: R.74, N.76, K.270, E.272, S.362 Ligands: ACT.19 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.74, C:N.76, C:N.76, C:K.270, C:E.272, C:S.362, C:S.362 GOL.18: 4 residues within 4Å: Chain C: N.229, P.457, E.458, R.461 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.229, C:R.461, C:R.461 GOL.24: 6 residues within 4Å: Chain D: R.74, N.76, K.270, E.272, S.362 Ligands: ACT.26 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.74, D:R.74, D:N.76, D:K.270, D:E.272, D:S.362, D:S.362 Water bridges: D:S.78, D:K.270 GOL.25: 4 residues within 4Å: Chain D: N.229, P.457, E.458, R.461 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.229, D:N.229, D:E.458, D:R.461

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 7 residues within 4Å: Chain A: T.51, R.74, N.76, H.79, S.362, G.363 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.51 Hydrogen bonds: A:N.76, A:S.362 Salt bridges: A:R.74 ACT.6: 3 residues within 4Å: Chain A: H.79, G.80, R.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.80 Salt bridges: A:H.79, A:R.198 ACT.7: 2 residues within 4Å: Chain A: R.93, Y.228 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.93 ACT.12: 8 residues within 4Å: Chain B: T.51, R.74, N.76, H.79, S.362, G.363, A.366 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.51 Hydrogen bonds: B:N.76, B:S.362 Salt bridges: B:R.74 ACT.13: 3 residues within 4Å: Chain B: H.79, G.80, R.198 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.79 Hydrogen bonds: B:G.80 Salt bridges: B:H.79, B:R.198 ACT.14: 5 residues within 4Å: Chain B: H.399, S.400, K.404 Chain C: H.396, H.421 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Salt bridges: B:H.399, B:K.404, C:H.396 ACT.19: 7 residues within 4Å: Chain C: T.51, R.74, N.76, H.79, S.362, G.363 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.51 Hydrogen bonds: C:N.76, C:S.362 Salt bridges: C:R.74 ACT.20: 3 residues within 4Å: Chain C: H.79, G.80, R.198 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.80 Salt bridges: C:H.79, C:R.198 ACT.21: 2 residues within 4Å: Chain C: R.93, Y.228 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.93 ACT.26: 8 residues within 4Å: Chain D: T.51, R.74, N.76, H.79, S.362, G.363, A.366 Ligands: GOL.24 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:T.51 Hydrogen bonds: D:N.76, D:S.362 Salt bridges: D:R.74 ACT.27: 3 residues within 4Å: Chain D: H.79, G.80, R.198 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:H.79 Hydrogen bonds: D:G.80 Salt bridges: D:H.79, D:R.198 ACT.28: 5 residues within 4Å: Chain A: H.396, H.421 Chain D: H.399, S.400, K.404 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Salt bridges: D:H.399, D:K.404, A:H.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, W.J. et al., Crystal structure of Cryptosporidium parvum pyruvate kinase. Plos One (2012)

Release Date

2012-10-17

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase

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