SMTL ID : 4b7u.1

PLASMODIUM FALCIPARUM L-LACTATE DEHYDROGENASE COMPLEXED WITH BICINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.127, H.182 Ligands: BCN.2 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain B: N.127, H.182 Ligands: BCN.7 No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain C: N.127, H.182 Ligands: BCN.11 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.182, H2O.22 CA.12: 3 residues within 4Å: Chain D: N.127, H.182 Ligands: BCN.13 No protein-ligand interaction detected (PLIP)

8 x BCN: BICINE(Non-covalent)

BCN.2: 8 residues within 4Å: Chain A: N.127, L.150, L.154, R.158, H.182, A.225, P.235 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.127, A:H.182 Water bridges: A:N.127, A:R.158, A:H.182 Salt bridges: A:R.158, A:H.182 BCN.7: 10 residues within 4Å: Chain B: V.125, N.127, L.150, L.154, R.158, H.182, A.225, S.234, P.235 Ligands: CA.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.127, B:H.182 Water bridges: B:N.127, B:R.158, B:H.182 Salt bridges: B:R.158, B:H.182 BCN.8: 6 residues within 4Å: Chain B: F.34, I.36, T.66, Y.67, E.108, H.112 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.67, B:H.112 Water bridges: B:D.68, B:D.68 Salt bridges: B:E.108, B:H.112 BCN.9: 3 residues within 4Å: Chain B: D.68, A.71, N.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.68 Salt bridges: B:D.68 BCN.11: 11 residues within 4Å: Chain C: V.125, N.127, L.150, L.154, R.158, H.182, A.225, S.234, P.235, P.239 Ligands: CA.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.127, C:H.182 Water bridges: C:N.127, C:R.158, C:H.182 Salt bridges: C:R.158, C:H.182 BCN.13: 9 residues within 4Å: Chain D: V.125, N.127, L.154, R.158, H.182, A.225, P.235, P.239 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.127 Water bridges: D:R.158, D:A.225 Salt bridges: D:R.158, D:H.182 BCN.14: 4 residues within 4Å: Chain D: A.73, D.74, N.119, K.146 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.74, D:K.146, D:Y.250, D:Y.250 BCN.15: 4 residues within 4Å: Chain D: G.13, M.14, T.83, S.234 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:M.14, D:T.83, D:T.83, D:S.234, D:S.234 Water bridges: D:G.13, D:I.15

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 2 residues within 4Å: Chain A: L.101, K.104 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.101 Hydrogen bonds: A:K.104

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: A.71, G.72 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: E.108, G.111, H.112 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain D: I.107, E.108, G.111, H.112 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birkinshaw, R.W. et al., The Crystal Structure of Plasmodium Falciparum L- Lactate Dehydrogenase in Complex with a Novel Bicine Ligand. To be Published

Release Date

2012-10-10

Peptides

L-LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-LACTATE DEHYDROGENASE

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