SMTL ID : 1gz4.1

molecular mechanism of the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: R.143, N.237, L.288, G.289, A.290, G.291, E.292, A.293, F.322, D.323, K.324, V.370, A.371, G.372, A.373, S.398 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.237, A:A.290, A:A.290, A:E.292, A:E.292, A:A.293, A:K.324, A:G.372, A:S.398 Water bridges: A:R.143, A:R.143, A:N.237, A:G.291 Salt bridges: A:R.143, A:R.143, A:R.143 ATP.2: 13 residues within 4Å: Chain A: H.132, K.134, G.170, I.171, R.172, R.175, I.457, L.458, N.460, R.520, Y.530, R.534 Chain D: D.222 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.132, A:K.134, A:G.170, A:R.172, A:R.175, A:N.460, A:Y.530, A:W.536, D:R.223 Water bridges: A:N.460 Salt bridges: A:H.132, A:R.175, A:R.520, A:R.534 pi-Cation interactions: A:R.175 ATP.6: 16 residues within 4Å: Chain B: R.143, L.145, N.237, L.288, G.289, A.290, G.291, E.292, A.293, D.323, K.324, V.370, A.371, G.372, A.373, S.398 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.237, B:A.290, B:A.290, B:E.292, B:E.292, B:E.292, B:A.293, B:K.324, B:K.324, B:K.324, B:G.372, B:S.398 Water bridges: B:R.143, B:R.143, B:G.291, B:A.294, B:N.399, B:N.399 Salt bridges: B:R.143, B:R.143 ATP.7: 12 residues within 4Å: Chain B: H.132, K.134, G.170, I.171, R.172, R.175, I.457, L.458, N.460, R.520, Y.530, R.534 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:H.132, B:G.170, B:R.172, B:R.175, B:N.460, B:Y.530, B:W.536 Salt bridges: B:H.132, B:R.175, B:R.520, B:R.534 pi-Cation interactions: B:R.175 ATP.11: 16 residues within 4Å: Chain C: R.143, L.145, N.237, L.288, G.289, A.290, G.291, E.292, A.293, D.323, K.324, V.370, A.371, G.372, A.373, S.398 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.237, C:A.290, C:A.290, C:E.292, C:E.292, C:A.293, C:K.324, C:K.324, C:K.324, C:G.372 Water bridges: C:G.291, C:A.294, C:D.323, C:N.399, C:N.399 Salt bridges: C:R.143, C:R.143 ATP.12: 14 residues within 4Å: Chain B: D.222 Chain C: H.132, K.134, G.170, I.171, R.172, R.175, I.457, L.458, N.460, R.520, Y.530, R.534, W.536 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:H.132, C:G.170, C:R.172, C:R.175, C:N.460, C:W.536 Salt bridges: C:H.132, C:R.520, C:R.534 pi-Cation interactions: C:R.175 ATP.16: 17 residues within 4Å: Chain D: R.143, N.237, L.288, G.289, A.290, G.291, E.292, A.293, F.322, D.323, K.324, V.370, A.371, G.372, A.373, L.376, S.398 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:N.237, D:A.290, D:A.290, D:E.292, D:E.292, D:E.292, D:A.293, D:K.324, D:G.372, D:S.398 Water bridges: D:N.237, D:G.291, D:A.294, D:D.323, D:D.323 Salt bridges: D:R.143, D:R.143 ATP.17: 13 residues within 4Å: Chain A: D.222 Chain D: H.132, K.134, G.170, I.171, R.172, R.175, I.457, L.458, N.460, R.520, Y.530, R.534 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:H.132, D:G.170, D:R.172, D:R.175, D:N.460, D:W.536 Water bridges: D:N.460 Salt bridges: D:H.132, D:R.175, D:R.520, D:R.534 pi-Cation interactions: D:R.175, D:R.175

4 x TTN: TARTRONATE(Non-covalent)

TTN.3: 11 residues within 4Å: Chain A: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.399, N.444, N.445 Ligands: MN.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.161, A:N.399, A:N.444, A:N.445, A:N.445 Water bridges: A:Y.90, A:Y.90 Salt bridges: A:R.143, A:K.161 TTN.8: 11 residues within 4Å: Chain B: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.399, N.444, N.445 Ligands: MN.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.145, B:K.161, B:N.399, B:N.444, B:N.445 Water bridges: B:N.445 Salt bridges: B:R.143, B:K.161 TTN.13: 11 residues within 4Å: Chain C: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.399, N.444, N.445 Ligands: MN.14 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.90, C:K.161, C:N.399, C:N.444, C:N.445 Water bridges: C:N.445 Salt bridges: C:R.143, C:K.161, C:K.161 TTN.18: 11 residues within 4Å: Chain D: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.399, N.444, N.445 Ligands: MN.19 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:L.145, D:K.161, D:N.399, D:N.444, D:N.445 Water bridges: D:Y.90, D:K.161, D:N.445 Salt bridges: D:R.143, D:K.161

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 5 residues within 4Å: Chain A: R.143, E.233, D.234, D.257 Ligands: TTN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.233, A:D.234, A:D.257, H2O.6 MN.9: 5 residues within 4Å: Chain B: R.143, E.233, D.234, D.257 Ligands: TTN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.233, B:D.234, B:D.257, H2O.12 MN.14: 6 residues within 4Å: Chain C: R.143, K.161, E.233, D.234, D.257 Ligands: TTN.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.233, C:D.234, C:D.257 MN.19: 5 residues within 4Å: Chain D: R.143, E.233, D.234, D.257 Ligands: TTN.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.233, D:D.234, D:D.257, H2O.22

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.5: 8 residues within 4Å: Chain A: Q.42, R.45, Y.62, I.66, R.69, L.73 Chain B: F.105, R.106 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.73 Water bridges: A:R.45, A:R.45, A:Y.62, A:Y.62 Salt bridges: A:R.45, A:R.69 FUM.10: 7 residues within 4Å: Chain A: F.105, R.106 Chain B: Q.42, R.45, I.66, R.69, L.73 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:F.105, B:E.37, B:Q.42, B:Y.62 Hydrophobic interactions: B:L.73 Salt bridges: B:R.45, B:R.69 FUM.15: 7 residues within 4Å: Chain C: Q.42, R.45, I.66, R.69, L.73 Chain D: F.105, R.106 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.73 Water bridges: C:Q.42, C:R.45, C:Y.62, C:N.70, D:F.105 Salt bridges: C:R.45, C:R.69 FUM.20: 7 residues within 4Å: Chain C: F.105, R.106 Chain D: Q.42, R.45, I.66, R.69, L.73 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.73 Water bridges: D:E.37, D:Q.42, D:Y.62, D:N.70, C:F.105 Salt bridges: D:R.45, D:R.69

Links

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Citation

Yang, Z. et al., Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)(+)-Dependent Malic Enzyme by ATP and Fumarate. Structure (2002)

Release Date

2002-07-25

Peptides

NAD-DEPENDENT MALIC ENZYME: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD-DEPENDENT MALIC ENZYME