SMTL ID : 1pjl.2 (1 other biounit)

Crystal structure of human m-NAD-ME in ternary complex with NAD and Lu3+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x LU: LUTETIUM (III) ION(Non-covalent)

LU.1: 3 residues within 4Å: Chain A: E.255, D.256, D.279 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.256 LU.4: 4 residues within 4Å: Chain B: L.167, E.255, D.256, D.279 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.256 LU.7: 3 residues within 4Å: Chain C: E.255, D.256, D.279 No protein-ligand interaction detected (PLIP) LU.10: 4 residues within 4Å: Chain D: K.183, E.255, D.256, D.279 No protein-ligand interaction detected (PLIP)

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 23 residues within 4Å: Chain A: R.165, N.259, T.283, L.310, G.311, A.312, G.313, E.314, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.283 Hydrogen bonds: A:A.312, A:A.312, A:G.313, A:A.315, A:D.345, A:K.346, A:N.421, A:N.421, A:N.421, A:G.465, A:N.467, A:N.467 Salt bridges: A:R.165, A:R.165 NAD.3: 12 residues within 4Å: Chain A: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, R.542, Y.552, R.556, W.558 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.154, A:K.156, A:R.194, A:R.197, A:R.197, A:R.556, A:W.558 Salt bridges: A:R.542, A:R.556 Water bridges: D:D.244 NAD.5: 23 residues within 4Å: Chain B: R.165, N.259, T.283, L.310, G.311, A.312, G.313, E.314, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.283 Hydrogen bonds: B:A.312, B:A.312, B:G.313, B:A.315, B:K.346, B:N.421, B:N.421, B:N.421, B:G.465 Salt bridges: B:R.165, B:R.165 NAD.6: 10 residues within 4Å: Chain B: H.154, G.192, I.193, R.194, R.197, I.479, L.480, R.542, R.556, W.558 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.154, B:R.194, B:R.197, B:R.197, B:R.556, B:W.558 Salt bridges: B:R.542, B:R.556 NAD.8: 22 residues within 4Å: Chain C: R.165, N.259, T.283, L.310, G.311, A.312, G.313, E.314, A.315, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.283 Hydrogen bonds: C:A.312, C:G.313, C:A.315, C:K.346, C:N.421, C:N.421, C:N.421, C:G.465, C:N.467, C:N.467 Salt bridges: C:R.165, C:R.165 NAD.9: 12 residues within 4Å: Chain C: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.194, C:R.194, C:R.197, C:R.197, C:Y.552, C:Y.552, C:R.556 Salt bridges: C:R.542, C:R.556, C:R.556 pi-Cation interactions: C:R.197 NAD.11: 22 residues within 4Å: Chain D: R.165, N.259, T.283, L.310, G.311, A.312, G.313, E.314, A.315, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:T.283 Hydrogen bonds: D:A.312, D:A.312, D:G.313, D:E.314, D:A.315, D:D.345, D:K.346, D:N.421, D:N.421, D:N.421, D:G.465 Salt bridges: D:R.165, D:R.165 NAD.12: 13 residues within 4Å: Chain D: K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, W.558, D.563 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.192, D:R.194, D:R.194, D:R.197, D:R.197, D:Y.552, D:W.558, D:D.563 Salt bridges: D:R.542, D:R.556, D:R.556 pi-Cation interactions: D:R.197, D:R.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Potent and competitive inhibition of malic enzymes by lanthanide ions. Biochem.Biophys.Res.Commun. (2000)

Release Date

2003-06-17

Peptides

NAD-dependent malic enzyme, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

NAD-dependent malic enzyme, mitochondrial

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