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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

LU.1: 4 residues within 4Å: Chain A: L.167, E.255, D.256, D.279 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.255, A:D.279 LU.4: 4 residues within 4Å: Chain B: L.167, E.255, D.256, D.279 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.255, B:D.256, B:D.279 LU.7: 4 residues within 4Å: Chain C: L.167, E.255, D.256, D.279 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.255, C:D.279 LU.10: 3 residues within 4Å: Chain D: E.255, D.256, D.279 No protein-ligand interaction detected (PLIP)

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

NAD.2: 22 residues within 4Å: Chain A: 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 A Hydrophobic interactions: A:T.283 Hydrogen bonds: A:A.312, A:A.312, A:G.313, A:A.315, A:K.346, A:N.421, A:N.421, A:N.421, A:G.465, A:N.467 Salt bridges: A:R.165, A:R.165 NAD.3: 14 residues within 4Å: Chain A: H.154, 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.192, A:R.194, A:R.197, A:R.197, A:Y.552, A:Y.552, A:W.558, A:D.563 Salt bridges: A:R.542, A:R.556 NAD.5: 21 residues within 4Å: Chain B: 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 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, B:N.467 Water bridges: B:G.313, B:A.316 Salt bridges: B:R.165 NAD.6: 12 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:K.156, B:R.194, B:R.197, B:R.197, B:Y.552, B:Y.552, B:R.556 Salt bridges: B:R.542, B:R.556, B:R.556 pi-Cation interactions: B:R.197 NAD.8: 21 residues within 4Å: Chain C: R.165, N.259, T.283, L.310, 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, C:A.315 Hydrogen bonds: C:A.312, C:A.312, C:G.313, C:A.315, C:K.346, C:N.421, C:N.421, C:N.421, C:G.465 Salt bridges: C:R.165, C:R.165 NAD.9: 11 residues within 4Å: Chain C: H.154, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.192, C:R.194, C:R.197, C:R.197, C:Y.552, C:Y.552 Water bridges: C:N.482 Salt bridges: C:R.542, C:R.556, C:R.556 NAD.11: 23 residues within 4Å: Chain D: 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 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:A.315, D:D.345, D:K.346, D:N.421, D:N.421, D:N.421, D:G.465, D:N.467 Salt bridges: D:R.165, D:R.165 NAD.12: 13 residues within 4Å: Chain D: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, W.558 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:H.154, D:G.192, D:R.194, D:R.197, D:R.197, D:Y.552, D:W.558 Salt bridges: D:R.542, D:R.556, D:R.556 pi-Cation interactions: 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
A

B
B

C
C

D
D

NAD-dependent malic enzyme, mitochondrial

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