SMTL ID : 4plg.1

Crystal structure of ancestral apicomplexan lactate dehydrogenase with oxamate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-tetramer

Ligands

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.1: 11 residues within 4Å: Chain A: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NA.6, NAI.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.99, A:R.99, A:N.131 Water bridges: A:S.240 Salt bridges: A:R.99, A:R.162, A:H.186 OXM.10: 10 residues within 4Å: Chain B: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAI.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.99, B:R.99, B:N.131 Water bridges: B:R.162, B:S.240, B:A.241, B:A.241 Salt bridges: B:R.99, B:R.162, B:H.186 OXM.13: 11 residues within 4Å: Chain C: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NA.18, NAI.21 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.99, C:R.99, C:N.131, C:H.186 Water bridges: C:S.240 Salt bridges: C:R.99, C:R.162, C:H.186 OXM.22: 10 residues within 4Å: Chain D: W.97, R.99, N.131, L.158, R.162, H.186, G.229, S.240, A.241 Ligands: NAI.24 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.99, D:R.99, D:N.131, D:H.186 Water bridges: D:R.162, D:S.240, D:A.241, D:A.241 Salt bridges: D:R.99, D:R.162, D:H.186

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

NA.2: 8 residues within 4Å: Chain A: G.15, S.16, G.17, M.18, I.19, G.20, T.83 Ligands: NAI.9 Ligand excluded by PLIP NA.3: 8 residues within 4Å: Chain A: L.13, I.14, G.15, G.20, M.23, I.81, I.82, T.83 Ligand excluded by PLIP NA.4: 8 residues within 4Å: Chain A: G.153, M.154, A.155, G.156, V.157, M.252, V.265, C.266 Ligand excluded by PLIP NA.5: 6 residues within 4Å: Chain A: G.156, V.182, I.183, G.184, V.265, G.282 Ligand excluded by PLIP NA.6: 7 residues within 4Å: Chain A: R.162, G.229, I.232, V.233, S.240, A.241 Ligands: OXM.1 Ligand excluded by PLIP NA.7: 8 residues within 4Å: Chain A: D.159, R.162, H.186, M.190, T.225, A.228, G.229 Ligands: NA.8 Ligand excluded by PLIP NA.8: 9 residues within 4Å: Chain A: R.99, R.162, M.190, T.225, K.226, N.227, A.228, G.229 Ligands: NA.7 Ligand excluded by PLIP NA.11: 6 residues within 4Å: Chain B: P.122, N.123, A.124, L.146, P.147, K.150 Ligand excluded by PLIP NA.14: 8 residues within 4Å: Chain C: G.15, S.16, G.17, M.18, I.19, G.20, T.83 Ligands: NAI.21 Ligand excluded by PLIP NA.15: 8 residues within 4Å: Chain C: L.13, I.14, G.15, G.20, M.23, I.81, I.82, T.83 Ligand excluded by PLIP NA.16: 8 residues within 4Å: Chain C: G.153, M.154, A.155, G.156, V.157, M.252, V.265, C.266 Ligand excluded by PLIP NA.17: 6 residues within 4Å: Chain C: G.156, V.182, I.183, G.184, V.265, G.282 Ligand excluded by PLIP NA.18: 7 residues within 4Å: Chain C: R.162, G.229, I.232, V.233, S.240, A.241 Ligands: OXM.13 Ligand excluded by PLIP NA.19: 8 residues within 4Å: Chain C: D.159, R.162, H.186, M.190, T.225, A.228, G.229 Ligands: NA.20 Ligand excluded by PLIP NA.20: 9 residues within 4Å: Chain C: R.99, R.162, M.190, T.225, K.226, N.227, A.228, G.229 Ligands: NA.19 Ligand excluded by PLIP NA.23: 6 residues within 4Å: Chain D: P.122, N.123, A.124, L.146, P.147, K.150 Ligand excluded by PLIP

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.9: 36 residues within 4Å: Chain A: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: OXM.1, NA.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.19, A:I.129, A:L.158, A:P.245 Hydrogen bonds: A:G.17, A:M.18, A:I.19, A:V.40, A:G.85, A:L.86, A:L.86, A:N.106, A:E.112, A:N.131, A:N.131, A:M.154 Water bridges: A:T.87, A:S.240 NAI.12: 35 residues within 4Å: Chain B: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: OXM.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.19, B:I.129, B:L.158, B:P.245 Hydrogen bonds: B:G.17, B:M.18, B:I.19, B:V.40, B:G.85, B:L.86, B:L.86, B:N.106, B:E.112, B:N.131, B:N.131, B:M.154 Water bridges: B:G.20, B:S.240 NAI.21: 36 residues within 4Å: Chain C: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: OXM.13, NA.14 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.19, C:I.129, C:L.158, C:P.245 Hydrogen bonds: C:G.17, C:M.18, C:I.19, C:V.40, C:G.85, C:L.86, C:L.86, C:N.106, C:E.112, C:N.131, C:N.131, C:M.154 Water bridges: C:T.87, C:S.240 NAI.24: 35 residues within 4Å: Chain D: I.14, G.15, S.16, G.17, M.18, I.19, G.20, F.38, D.39, V.40, V.41, M.44, Y.71, T.83, A.84, G.85, L.86, T.87, L.102, N.106, I.109, E.112, I.129, T.130, N.131, L.133, M.154, A.155, L.158, H.186, S.240, A.241, Y.242, P.245 Ligands: OXM.22 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.19, D:I.129, D:L.158, D:P.245 Hydrogen bonds: D:G.17, D:M.18, D:I.19, D:V.40, D:G.85, D:L.86, D:L.86, D:N.106, D:E.112, D:N.131, D:N.131, D:M.154 Water bridges: D:G.20, D:S.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boucher, J.I. et al., An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. Elife (2014)

Release Date

2014-07-02

Peptides

lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

lactate dehydrogenase

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