SMTL ID : 1efk.1

STRUCTURE OF HUMAN MALIC ENZYME IN COMPLEX WITH KETOMALONATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: R.165, E.255, D.256, D.279 Ligands: MAK.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.255, A:D.256, A:D.279, H2O.1 MG.5: 5 residues within 4Å: Chain B: R.165, E.255, D.256, D.279 Ligands: MAK.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.255, B:D.256, B:D.279, H2O.2 MG.9: 6 residues within 4Å: Chain C: R.165, K.183, E.255, D.256, D.279 Ligands: MAK.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.255, C:D.256, C:D.279, H2O.3 MG.13: 5 residues within 4Å: Chain D: R.165, E.255, D.256, D.279 Ligands: MAK.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.255, D:D.256, D:D.279, H2O.3

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

NAD.2: 26 residues within 4Å: Chain A: R.165, L.167, G.168, N.259, D.279, 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.419, S.420, N.421, G.446, G.465, N.466, N.467 Ligands: MAK.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.283 Hydrogen bonds: A:R.165, A:L.167, A:N.259, A:A.312, A:E.314, A:E.314, A:A.315, A:K.346, A:L.419, A:N.421, A:N.421, A:N.467 Water bridges: A:A.316 Salt bridges: A:R.165 NAD.3: 15 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 Chain D: D.244, R.245, G.247 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.154, A:K.156, A:G.192, A:R.194, A:R.197, A:R.197, A:N.482, A:Y.552 Salt bridges: A:R.542, A:R.556 pi-Cation interactions: A:R.194 NAD.6: 27 residues within 4Å: Chain B: R.165, L.167, G.168, N.259, D.279, T.283, 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.466, N.467 Ligands: MAK.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.283 Hydrogen bonds: B:L.167, B:N.259, B:A.312, B:A.312, B:E.314, B:E.314, B:A.315, B:D.345, B:K.346, B:L.419, B:N.421, B:N.421, B:N.467 Salt bridges: B:R.165 NAD.7: 14 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 Chain C: D.244, R.245 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.154, B:K.156, B:G.192, B:R.194, B:N.482, B:Y.552, B:Y.552, C:R.245 Salt bridges: B:R.542, B:R.556 NAD.10: 26 residues within 4Å: Chain C: R.165, L.167, G.168, N.259, D.279, T.283, 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.419, S.420, N.421, G.446, G.465, N.466, N.467 Ligands: MAK.12 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:T.283 Hydrogen bonds: C:L.167, C:N.259, C:A.312, C:A.312, C:E.314, C:A.315, C:D.345, C:K.346, C:K.346, C:L.419, C:N.421, C:N.467 Salt bridges: C:R.165 NAD.11: 13 residues within 4Å: Chain B: D.244, R.245 Chain C: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, R.542, Y.552, R.556 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.154, C:K.156, C:G.192, C:R.194, C:Y.552, B:R.245 Salt bridges: C:R.542, C:R.556 NAD.14: 27 residues within 4Å: Chain D: R.165, L.167, G.168, N.259, D.279, 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.466, N.467 Ligands: MAK.16 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:T.283 Hydrogen bonds: D:L.167, D:N.259, D:A.312, D:E.314, D:E.314, D:A.315, D:K.346, D:L.419, D:N.421, D:N.421, D:N.467 Salt bridges: D:R.165 NAD.15: 15 residues within 4Å: Chain A: D.244, R.245, G.247 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 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.154, D:G.192, D:R.194, D:R.197, D:R.197, D:N.482, D:Y.552 Salt bridges: D:R.542, D:R.556

4 x MAK: ALPHA-KETOMALONIC ACID(Non-covalent)

MAK.4: 12 residues within 4Å: Chain A: Y.112, R.165, L.167, K.183, E.255, D.256, D.279, N.421, N.466, N.467 Ligands: MG.1, NAD.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.167, A:K.183, A:E.255, A:N.421, A:N.466, A:N.467, A:N.467 Salt bridges: A:R.165, A:K.183 MAK.8: 13 residues within 4Å: Chain B: Y.112, R.165, L.167, K.183, E.255, D.256, D.278, D.279, N.421, N.466, N.467 Ligands: MG.5, NAD.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.112, B:L.167, B:K.183, B:D.278, B:N.421, B:N.467, B:N.467, B:N.467 Water bridges: B:E.255, B:E.255 Salt bridges: B:R.165, B:K.183, B:K.183 MAK.12: 13 residues within 4Å: Chain C: Y.112, R.165, L.167, K.183, E.255, D.256, D.278, D.279, N.421, N.466, N.467 Ligands: MG.9, NAD.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.112, C:L.167, C:K.183, C:N.466, C:N.467, C:N.467 Salt bridges: C:R.165, C:K.183, C:K.183 MAK.16: 12 residues within 4Å: Chain D: Y.112, R.165, L.167, K.183, E.255, D.256, D.279, N.421, N.466, N.467 Ligands: MG.13, NAD.14 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.112, D:L.167, D:K.183, D:N.421, D:N.466, D:N.467, D:N.467 Salt bridges: D:R.165, D:K.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Structure of a closed form of human malic enzyme and implications for catalytic mechanism. Nat.Struct.Biol. (2000)

Release Date

2000-03-08

Peptides

MALIC ENZYME: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

MALIC ENZYME

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