SMTL ID : 8eyo.1

Crystal Structure of Human Mitochondrial NADP+ Malic Enzyme 3 with NADP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: L.148, N.240, T.264, Q.291, G.292, A.293, G.294, E.295, A.296, V.325, D.326, S.327, K.342, V.370, A.371, A.372, I.373, L.397, S.398, N.399, G.424, G.443, N.445 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.264 Hydrogen bonds: A:Q.291, A:A.293, A:A.293, A:E.295, A:A.296, A:S.327, A:S.327, A:S.327, A:S.398, A:N.399, A:N.399, A:N.399, A:G.443 Water bridges: A:A.297, A:N.445 Salt bridges: A:K.342 NAP.3: 24 residues within 4Å: Chain B: R.146, N.240, T.264, Q.291, G.292, A.293, G.294, E.295, A.296, V.325, D.326, S.327, K.328, K.342, V.370, A.371, A.372, I.373, L.397, S.398, N.399, G.424, G.443, N.445 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.264 Hydrogen bonds: B:Q.291, B:A.293, B:A.293, B:E.295, B:A.296, B:S.327, B:S.327, B:S.327, B:N.399, B:N.399, B:G.443 Water bridges: B:R.146, B:G.294, B:A.297, B:G.329, B:K.342, B:K.342 Salt bridges: B:R.146, B:K.328, B:K.342 NAP.5: 23 residues within 4Å: Chain C: L.148, N.240, T.264, Q.291, G.292, A.293, G.294, E.295, A.296, V.325, D.326, S.327, K.342, V.370, A.371, A.372, I.373, L.397, S.398, N.399, G.424, G.443, N.445 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:T.264 Hydrogen bonds: C:Q.291, C:A.293, C:A.293, C:E.295, C:A.296, C:S.327, C:S.327, C:S.327, C:S.398, C:N.399, C:N.399, C:N.399, C:G.443 Water bridges: C:A.297, C:N.445 Salt bridges: C:K.342 NAP.7: 24 residues within 4Å: Chain D: R.146, N.240, T.264, Q.291, G.292, A.293, G.294, E.295, A.296, V.325, D.326, S.327, K.328, K.342, V.370, A.371, A.372, I.373, L.397, S.398, N.399, G.424, G.443, N.445 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:T.264 Hydrogen bonds: D:Q.291, D:A.293, D:A.293, D:E.295, D:A.296, D:S.327, D:S.327, D:S.327, D:N.399, D:N.399, D:G.443 Water bridges: D:R.146, D:G.294, D:A.297, D:G.329, D:K.342, D:K.342 Salt bridges: D:R.146, D:K.328, D:K.342

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 9 residues within 4Å: Chain A: G.18, M.19, L.40, Q.45, R.48, I.49, R.72, L.76 Chain C: R.109 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.76 Hydrogen bonds: A:M.19, A:Q.45, A:R.48 Water bridges: A:N.73 Salt bridges: A:R.48, A:R.72, C:R.109, C:R.109 CIT.4: 8 residues within 4Å: Chain B: G.18, M.19, L.40, Q.45, R.48, R.72, L.76 Chain D: R.109 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.76 Hydrogen bonds: B:M.19, B:Q.45, B:R.48 Salt bridges: B:R.48, B:R.72, D:R.109, D:R.109 CIT.6: 9 residues within 4Å: Chain A: R.109 Chain C: G.18, M.19, L.40, Q.45, R.48, I.49, R.72, L.76 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.76 Hydrogen bonds: C:M.19, C:Q.45, C:R.48 Water bridges: C:N.73 Salt bridges: C:R.48, C:R.72, A:R.109, A:R.109 CIT.8: 8 residues within 4Å: Chain B: R.109 Chain D: G.18, M.19, L.40, Q.45, R.48, R.72, L.76 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D Salt bridges: B:R.109, B:R.109, D:R.48, D:R.72 Hydrophobic interactions: D:L.76 Hydrogen bonds: D:M.19, D:Q.45, D:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grell, T.A.J. et al., Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer. Heliyon (2022)

Release Date

2023-02-08

Peptides

NADP-dependent malic enzyme, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NADP-dependent malic enzyme, mitochondrial

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