SMTL ID : 1do8.1

CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 12 residues within 4Å: Chain A: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.2, NAD.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.401, A:N.446, A:N.447 Water bridges: A:Y.92, A:K.163 Salt bridges: A:R.145, A:K.163 OXL.5: 12 residues within 4Å: Chain B: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.6, NAD.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.401, B:N.446, B:N.447 Salt bridges: B:R.145, B:K.163 OXL.9: 12 residues within 4Å: Chain C: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.10, NAD.11 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.401, C:N.446, C:N.447 Water bridges: C:K.163, C:K.163 Salt bridges: C:R.145, C:K.163, C:K.163 OXL.13: 12 residues within 4Å: Chain D: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.14, NAD.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.401, D:N.446, D:N.447 Salt bridges: D:R.145, D:K.163

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

MN.2: 5 residues within 4Å: Chain A: R.145, E.235, D.236, D.259 Ligands: OXL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.235, A:D.236, A:D.259, H2O.1 MN.6: 5 residues within 4Å: Chain B: R.145, E.235, D.236, D.259 Ligands: OXL.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.235, B:D.236, B:D.259, H2O.10 MN.10: 6 residues within 4Å: Chain C: R.145, K.163, E.235, D.236, D.259 Ligands: OXL.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.235, C:D.236, C:D.259, H2O.17 MN.14: 5 residues within 4Å: Chain D: R.145, E.235, D.236, D.259 Ligands: OXL.13 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.235, D:D.236, D:D.259, H2O.28

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

NAD.3: 28 residues within 4Å: Chain A: R.145, L.147, G.148, N.239, D.259, T.263, L.290, G.291, A.292, G.293, E.294, A.295, F.324, D.325, K.326, V.372, A.373, G.374, A.375, L.378, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: OXL.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.263 Hydrogen bonds: A:L.147, A:N.239, A:A.292, A:A.292, A:E.294, A:A.295, A:K.326, A:L.399, A:N.401, A:N.401, A:N.447 Water bridges: A:G.293, A:A.296, A:K.326 Salt bridges: A:R.145 NAD.4: 16 residues within 4Å: Chain A: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536 Chain D: D.224, R.225, Y.226, G.227 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:H.134, A:G.172, A:R.174, A:R.177, A:R.177, A:N.462, A:Y.532, A:Y.532 Water bridges: A:K.136, A:R.536 Salt bridges: A:R.522, A:R.536 pi-Cation interactions: A:R.177 NAD.7: 28 residues within 4Å: Chain B: R.145, L.147, G.148, N.239, D.259, T.263, L.290, G.291, A.292, G.293, E.294, A.295, F.324, D.325, K.326, V.372, A.373, G.374, A.375, L.378, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: OXL.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.263 Hydrogen bonds: B:L.147, B:N.239, B:A.292, B:A.292, B:E.294, B:E.294, B:A.295, B:K.326, B:K.326, B:L.399, B:N.401, B:N.401, B:N.447 Water bridges: B:N.239, B:G.293, B:G.293, B:A.296 Salt bridges: B:R.145 NAD.8: 14 residues within 4Å: Chain B: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536 Chain C: D.224, R.225 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:H.134, B:K.136, B:R.174, B:R.177, B:N.462, B:Y.532, B:Y.532, B:R.536 Water bridges: B:N.462 Salt bridges: B:R.522, B:R.536 pi-Cation interactions: B:R.177, B:R.177 NAD.11: 27 residues within 4Å: Chain C: R.145, L.147, G.148, N.239, D.259, T.263, L.290, G.291, A.292, G.293, E.294, A.295, F.324, D.325, K.326, V.372, A.373, G.374, A.375, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: OXL.9 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:T.263 Hydrogen bonds: C:L.147, C:N.239, C:A.292, C:A.292, C:E.294, C:A.295, C:D.325, C:K.326, C:K.326, C:L.399, C:N.401, C:N.401, C:N.446, C:N.447 Water bridges: C:G.293, C:A.296 Salt bridges: C:R.145 NAD.12: 14 residues within 4Å: Chain B: D.224, R.225 Chain C: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.172, C:R.174, C:R.177, C:N.462, C:Y.532, C:W.538, B:R.225 Salt bridges: C:R.522, C:R.536 pi-Cation interactions: C:R.177 NAD.15: 28 residues within 4Å: Chain D: R.145, L.147, G.148, N.239, D.259, T.263, L.290, G.291, A.292, G.293, E.294, A.295, F.324, D.325, K.326, V.372, A.373, G.374, A.375, L.378, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: OXL.13 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.263 Hydrogen bonds: D:L.147, D:N.239, D:A.292, D:A.292, D:E.294, D:E.294, D:A.295, D:K.326, D:L.399, D:N.401, D:N.401, D:N.446, D:N.447 Water bridges: D:N.239, D:G.293, D:A.296, D:D.325, D:A.375 Salt bridges: D:R.145 NAD.16: 15 residues within 4Å: Chain A: D.224, R.225, G.227 Chain D: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:H.134, D:G.172, D:R.174, D:R.177, D:N.462, D:Y.532 Water bridges: D:N.133, D:N.462 Salt bridges: D:R.522, D:R.536 pi-Cation interactions: D:R.177

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

2000-03-06

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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