SMTL ID : 1gq2.3 (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 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:D.257, A:T.261 Hydrogen bonds: A:R.143, A:L.145, A:N.237, A:Q.288, A:A.290, A:A.290, A:E.292, A:E.292, A:A.293, A:D.323, A:S.324, A:S.324, A:N.396, A:N.396, A:N.442, A:N.442 Water bridges: A:N.237, A:K.339 Salt bridges: A:R.143, A:K.339 NAP.11: 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.12 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.261 Hydrogen bonds: B:N.237, B:A.290, B:A.290, B:E.292, B:A.293, B:S.324, B:S.324, B:N.396, B:N.396, B:N.396, B:N.441, B:N.442, B:N.442 Salt bridges: B:R.143, B:K.339 NAP.18: 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.19 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:T.261 Hydrogen bonds: C:N.237, C:A.290, C:A.290, C:E.292, 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.23: 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.24 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.261 Hydrogen bonds: D:N.237, D:A.290, D:A.290, D:E.292, D:E.292, D:A.293, D:S.324, D:S.324, D:S.324, D:N.396, D:N.396, D:N.396, D:N.442, D:N.442 Water bridges: 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.256, D.257, N.396, N.441, N.442 Ligands: NAP.1, MN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.90, A:N.396, A:N.441, A:N.442 Salt bridges: A:R.143, A:K.161, A:K.161 OXL.12: 12 residues within 4Å: Chain B: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.396, N.441, N.442 Ligands: NAP.11, MN.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.396, B:N.441, B:N.442 Water bridges: B:K.161, B:K.161 Salt bridges: B:R.143, B:K.161, B:K.161 OXL.19: 12 residues within 4Å: Chain C: Y.90, R.143, L.145, K.161, E.233, D.234, D.257, N.396, N.441, N.442 Ligands: NAP.18, MN.20 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.396, C:N.441, C:N.442 Salt bridges: C:R.143, C:K.161 OXL.24: 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.23, MN.25 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.396, D:N.441, D:N.442 Water bridges: D:K.161, D:K.161, D:K.161, D:K.161 Salt bridges: D:R.143, D:K.161

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

MN.3: 5 residues within 4Å: Chain A: K.161, E.233, D.234, D.257 Ligands: OXL.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.233, A:D.234, A:D.257 MN.13: 4 residues within 4Å: Chain B: E.233, D.234, D.257 Ligands: OXL.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.233, B:D.234, B:D.257, H2O.143 MN.20: 4 residues within 4Å: Chain C: E.233, D.234, D.257 Ligands: OXL.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.233, C:D.234, C:D.257 MN.25: 5 residues within 4Å: Chain D: R.143, E.233, D.234, D.257 Ligands: OXL.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.233, D:D.234, D:D.257, H2O.259

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

NA.4: 4 residues within 4Å: Chain A: W.320, M.321, I.328, F.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.342 NA.5: 2 residues within 4Å: Chain A: E.308, G.309 No protein-ligand interaction detected (PLIP) NA.14: 6 residues within 4Å: Chain B: F.418, P.437, G.438, G.485, R.486, L.487 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.418, B:G.438, B:L.487 NA.15: 5 residues within 4Å: Chain B: M.86, Y.90, T.91, P.423, Q.439 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.439, B:Q.439 NA.21: 5 residues within 4Å: Chain C: Y.196, I.197, G.198, R.200 Chain D: C.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.200 NA.26: 6 residues within 4Å: Chain D: Y.444, V.445, P.447, G.448, S.498, I.501 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.445, D:G.448

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

CL.6: 6 residues within 4Å: Chain A: D.234, F.235, A.240, N.255, D.257, E.292 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: D.425 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.248, N.249, I.461, G.462 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: T.276, K.387, R.388 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.248, G.462, D.463 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: R.107 Chain B: S.65, R.69 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: R.106 Chain B: L.62, S.65 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain C: H.245, R.248 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain D: N.481, P.490 Ligand excluded by PLIP

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
I

B
J

C
K

D
L

MALIC ENZYME

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