SMTL ID : 1gq2.2 (3 other biounits)

MALIC ENZYME FROM PIGEON LIVER

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: R.143, L.145, G.146, N.237, D.257, T.261, Q.288, G.289, A.290, G.291, E.292, A.293, V.322, D.323, S.324, K.339, V.367, A.368, A.369, I.370, L.394, S.395, N.396, G.421, G.440, N.441, N.442 Ligands: OXL.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.237, A:T.261, A:Q.288, A:A.290, A:A.290, A:E.292, A:A.293, A:S.324, A:S.324, A:S.324, A:N.396, A:N.396, A:N.396, A:N.442, A:N.442 Water bridges: A:G.291, A:G.291, A:K.339, A:K.339 Salt bridges: A:R.143, A:K.339 NAP.7: 28 residues within 4Å: Chain B: R.143, L.145, G.146, N.237, D.257, T.261, Q.288, G.289, A.290, G.291, E.292, A.293, V.322, D.323, S.324, K.339, V.367, A.368, A.369, I.370, L.394, S.395, N.396, G.421, G.440, N.441, N.442 Ligands: OXL.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.261 Hydrogen bonds: B:N.237, B:Q.288, B:A.290, B:A.290, B:E.292, B:E.292, B:A.293, B:D.323, B:S.324, B:S.324, B:N.396, B:N.396, B:N.396, B:N.442, B:N.442 Salt bridges: B:R.143, B:K.339 NAP.14: 28 residues within 4Å: Chain C: R.143, L.145, G.146, N.237, D.257, T.261, Q.288, G.289, A.290, G.291, E.292, A.293, V.322, D.323, S.324, K.339, V.367, A.368, A.369, I.370, L.394, S.395, N.396, G.421, G.440, N.441, N.442 Ligands: OXL.15 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:D.257, C:T.261 Hydrogen bonds: C:N.237, C:A.290, C:A.290, C:E.292, C:A.293, C:D.323, C:S.324, C:S.324, C:N.396, C:N.396, C:N.396, C:N.442, C:N.442 Salt bridges: C:R.143, C:K.339 NAP.19: 28 residues within 4Å: Chain D: R.143, L.145, G.146, N.237, D.257, T.261, Q.288, G.289, A.290, G.291, E.292, A.293, V.322, D.323, S.324, K.339, V.367, A.368, A.369, I.370, L.394, S.395, N.396, G.421, G.440, N.441, N.442 Ligands: OXL.20 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.261 Hydrogen bonds: D:N.237, D:Q.288, D:A.290, D:A.290, D:E.292, D:A.293, D:S.324, D:S.324, D:N.396, D:N.396, D:N.396, D:N.442, D:N.442 Water bridges: D:G.291, D:A.294 Salt bridges: D:R.143, D:K.339

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 13 residues within 4Å: Chain A: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.396, N.441, N.442 Ligands: NAP.1, MN.3, CL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.396, A:N.441, A:N.442 Water bridges: A:K.161, A:K.161 Salt bridges: A:R.143, A:K.161 OXL.8: 12 residues within 4Å: Chain B: R.143, L.145, K.161, E.233, D.234, D.257, N.396, N.441, N.442 Ligands: NAP.7, MN.9, CL.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.256, B:N.396, B:N.441, B:N.442 Salt bridges: B:R.143, B:K.161, B:K.161 OXL.15: 11 residues within 4Å: Chain C: R.143, L.145, K.161, E.233, D.234, D.257, N.396, N.441, N.442 Ligands: NAP.14, MN.16 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.257, C:N.396, C:N.441, C:N.442 Water bridges: C:K.161 Salt bridges: C:R.143, C:K.161 OXL.20: 12 residues within 4Å: Chain D: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.396, N.441, N.442 Ligands: NAP.19, MN.21 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.396, D:N.441, D:N.442 Salt bridges: D:R.143, D:K.161, D:K.161

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

MN.3: 5 residues within 4Å: Chain A: R.143, E.233, D.234, D.257 Ligands: OXL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.233, A:D.234, A:D.257, H2O.58 MN.9: 4 residues within 4Å: Chain B: E.233, D.234, D.257 Ligands: OXL.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.136 MN.16: 5 residues within 4Å: Chain C: K.161, E.233, D.234, D.257 Ligands: OXL.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.233, C:D.234, C:D.257 MN.21: 5 residues within 4Å: Chain D: K.161, E.233, D.234, D.257 Ligands: OXL.20 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.233, D:E.233, D:D.234, D:D.257

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: D.140, E.142, Y.209, F.235, A.236, N.239 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: Q.39, D.536, Y.537 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: Y.90, L.145, I.157, K.161 Ligands: OXL.2 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: Y.90, T.91, L.145, K.161 Ligands: OXL.8 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: G.15, M.16, Q.42 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: Y.533, S.534 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain D: Q.380, A.383, A.384, R.415 Ligand excluded by PLIP

8 x NA: SODIUM ION(Non-functional Binders)

NA.10: 3 residues within 4Å: Chain B: L.458, N.512, T.514 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.512, B:T.514, B:T.514 NA.11: 4 residues within 4Å: Chain B: M.64, D.68, R.107, R.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.68 NA.17: 8 residues within 4Å: Chain C: L.7, R.8, D.9, P.10, N.13, D.68, R.69 Chain D: R.107 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.7, D:R.107 NA.22: 5 residues within 4Å: Chain D: M.86, Y.90, T.91, P.423, Q.439 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.91, D:Q.439 NA.23: 6 residues within 4Å: Chain D: G.95, L.96, Q.99, L.147, P.397 Ligands: NA.25 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.95 Water bridges: D:L.96 NA.24: 3 residues within 4Å: Chain D: L.280, A.304, E.308 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.308 NA.25: 2 residues within 4Å: Chain D: S.399 Ligands: NA.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.399, D:S.399 Water bridges: D:S.399 NA.26: 7 residues within 4Å: Chain D: Q.288, V.367, A.368, A.369, I.370, S.395, E.402 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.368, D:I.370, D:S.395, D:S.395, D:E.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Structural Studies of the Pigeon Cytosolic Nadp+ -Dependent Malic Enzyme. Protein Sci. (2002)

Release Date

2002-05-23

Peptides

MALIC ENZYME: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

MALIC ENZYME

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