SMTL ID : 3nv9.1

Crystal structure of Entamoeba histolytica Malic Enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.183, K.377, T.379, D.380 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.380 Water bridges: A:R.183, A:Q.196, A:N.381 Salt bridges: A:R.183, A:K.377 SO4.2: 4 residues within 4Å: Chain A: Q.30, K.33, K.483 Chain B: R.71 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.30, A:Q.30 Salt bridges: A:K.33, A:K.483, B:R.71 Water bridges: B:T.74, B:T.74 SO4.3: 2 residues within 4Å: Chain A: R.453, Q.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.457 Salt bridges: A:R.453 SO4.4: 2 residues within 4Å: Chain A: S.20, Q.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:E.340 Water bridges: A:E.22 SO4.5: 7 residues within 4Å: Chain A: Q.172, G.226, A.227, G.228, F.251, D.252, S.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.172, A:A.227, A:S.253, A:S.253 Salt bridges: A:K.273 SO4.6: 2 residues within 4Å: Chain A: K.5, A.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.6 SO4.7: 2 residues within 4Å: Chain A: R.376, R.432 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.374 Water bridges: A:D.81, A:R.374 Salt bridges: A:R.376, A:R.432 SO4.15: 4 residues within 4Å: Chain B: R.183, K.377, T.379, D.380 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.380 Water bridges: B:R.183, B:Q.196, B:T.379, B:N.381 Salt bridges: B:R.183 SO4.16: 6 residues within 4Å: Chain B: Q.172, A.227, G.228, D.252, S.253 Ligands: GOL.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.227, B:S.253, B:S.253 Salt bridges: B:K.273 SO4.17: 2 residues within 4Å: Chain B: S.20, Q.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.21 Water bridges: B:S.20 SO4.18: 3 residues within 4Å: Chain A: R.71 Chain B: Q.30, K.33 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.30, A:R.71 Salt bridges: B:K.33 Water bridges: A:S.70 SO4.19: 2 residues within 4Å: Chain B: P.411, R.453 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.126, B:Y.126 Salt bridges: B:R.453 SO4.20: 6 residues within 4Å: Chain B: F.393, D.409, E.410, P.411, G.412, I.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.412, B:I.413 SO4.21: 5 residues within 4Å: Chain B: N.75, N.79, S.82, F.85, Y.86 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.79, B:S.82, B:S.82 Water bridges: A:E.37 SO4.22: 1 residues within 4Å: Chain B: K.315 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.315

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

NA.8: 6 residues within 4Å: Chain A: T.348, R.350, F.353, P.354, N.355, Q.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.348, A:R.350, A:F.353 NA.23: 6 residues within 4Å: Chain B: T.348, R.350, F.353, P.354, N.355, Q.356 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.348, B:R.350, B:R.350

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: S.287, I.288, A.289, K.310, E.312, W.313 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.287, A:I.288, A:A.289, A:K.310, A:E.312, A:E.312 GOL.10: 7 residues within 4Å: Chain A: R.101, I.170, S.171, Q.172, G.228, S.229, T.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.172, A:Q.172, A:S.229, A:S.229, A:T.303 GOL.11: 4 residues within 4Å: Chain A: P.148, N.174, K.177, R.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.173 Water bridges: A:K.177 GOL.12: 8 residues within 4Å: Chain A: L.103, V.116, K.120, D.169, N.358, N.359 Chain B: Y.65, T.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.120, A:D.169, A:N.359 Water bridges: A:T.198, A:N.359 GOL.14: 6 residues within 4Å: Chain A: E.153, R.157 Chain B: N.141, K.142, E.143, D.147 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.142, A:R.157 GOL.24: 9 residues within 4Å: Chain B: Q.172, Y.176, A.227, T.232, R.269, F.270, Y.271, R.272, K.273 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.172, B:Y.176, B:A.227, B:R.269, B:F.270, B:R.272, B:K.273 GOL.25: 5 residues within 4Å: Chain B: R.101, Q.172, G.228, S.229 Ligands: SO4.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.101, B:S.229, B:S.229 Water bridges: B:R.101, B:Q.172, B:S.230 GOL.28: 8 residues within 4Å: Chain A: Y.65, T.66 Chain B: L.103, V.116, K.120, D.169, N.358, N.359 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.120, B:D.169, B:N.358, B:N.358, A:T.66 Water bridges: B:L.103, B:N.359, B:N.359

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

ACT.13: 5 residues within 4Å: Chain A: D.81, L.84, R.89, D.187, R.374 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.84 Water bridges: A:R.374 Salt bridges: A:R.89, A:R.374, A:R.432 ACT.26: 5 residues within 4Å: Chain B: N.80, D.81, D.187, R.374, R.432 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.80 Water bridges: B:R.374 Salt bridges: B:R.89, B:R.374, B:R.432 ACT.27: 6 residues within 4Å: Chain B: G.90, N.91, K.368, L.371, I.444, D.448 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.90, B:N.91 Salt bridges: B:K.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chakrabarty, A. et al., Structural and functional characterization of Entamoeba histolytica Malic enzyme. To be Published

Release Date

2011-07-20

Peptides

Malic enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malic enzyme