SMTL ID : 1nfb.2 (1 other biounit)

Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP and NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x CPR: 6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE(Covalent)

CPR.1: 19 residues within 4Å: Chain A: S.68, M.70, R.322, S.327, G.328, S.329, I.330, C.331, E.335, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Y.411 Ligands: NAD.2 14 PLIP interactions: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.68, A:R.322, A:S.329, A:D.364, A:G.366, A:I.367, A:G.387, A:S.388, A:S.388, A:S.388 Water bridges: A:N.303, A:C.331, ?.1, ?.1 CPR.3: 19 residues within 4Å: Chain B: S.68, M.70, R.322, S.327, G.328, S.329, I.330, C.331, E.335, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Y.411 Ligands: NAD.4 14 PLIP interactions: 12 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.68, B:R.322, B:S.329, B:D.364, B:G.366, B:I.367, B:G.387, B:S.388, B:S.388, B:S.388 Water bridges: B:N.303, B:C.331, ?.3, ?.3 CPR.5: 19 residues within 4Å: Chain C: S.68, M.70, R.322, S.327, G.328, S.329, I.330, C.331, E.335, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Y.411 Ligands: NAD.6 14 PLIP interactions: 12 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:S.68, C:R.322, C:S.329, C:D.364, C:G.366, C:I.367, C:G.387, C:S.388, C:S.388, C:S.388 Water bridges: C:N.303, C:C.331, ?.5, ?.5 CPR.7: 19 residues within 4Å: Chain D: S.68, M.70, R.322, S.327, G.328, S.329, I.330, C.331, E.335, D.364, G.365, G.366, I.367, M.385, M.386, G.387, S.388, Y.411 Ligands: NAD.8 14 PLIP interactions: 12 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:S.68, D:R.322, D:S.329, D:D.364, D:G.366, D:I.367, D:G.387, D:S.388, D:S.388, D:S.388 Water bridges: D:N.303, D:C.331, ?.7, ?.7

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

NAD.2: 13 residues within 4Å: Chain A: T.252, H.253, D.274, S.275, S.276, F.282, N.303, R.322 Chain D: F.44, T.45, H.466, Q.469 Ligands: CPR.1 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:T.252, A:T.252, A:E.254, A:D.274, A:S.275, A:S.276, A:S.276, A:R.322, A:R.322, D:Q.469, D:Q.469 Water bridges: A:S.275, A:Q.277, D:H.466 pi-Stacking: A:H.253, A:F.282, A:F.282 Salt bridges: D:H.466 NAD.4: 13 residues within 4Å: Chain B: T.252, H.253, D.274, S.275, S.276, F.282, N.303, R.322 Chain C: F.44, T.45, H.466, Q.469 Ligands: CPR.3 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:T.252, B:T.252, B:E.254, B:D.274, B:S.275, B:S.276, B:S.276, B:R.322, B:R.322, C:Q.469, C:Q.469 Water bridges: B:S.275, B:Q.277, C:H.466 pi-Stacking: B:H.253, B:F.282, B:F.282 Salt bridges: C:H.466 NAD.6: 13 residues within 4Å: Chain A: F.44, T.45, H.466, Q.469 Chain C: T.252, H.253, D.274, S.275, S.276, F.282, N.303, R.322 Ligands: CPR.5 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:T.252, C:T.252, C:E.254, C:D.274, C:S.275, C:S.276, C:S.276, C:R.322, C:R.322, A:Q.469, A:Q.469 Water bridges: C:S.275, C:Q.277, A:H.466 pi-Stacking: C:H.253, C:F.282, C:F.282 Salt bridges: A:H.466 NAD.8: 13 residues within 4Å: Chain B: F.44, T.45, H.466, Q.469 Chain D: T.252, H.253, D.274, S.275, S.276, F.282, N.303, R.322 Ligands: CPR.7 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain D Hydrogen bonds: B:Q.469, B:Q.469, D:T.252, D:T.252, D:E.254, D:D.274, D:S.275, D:S.276, D:S.276, D:R.322, D:R.322 Water bridges: B:H.466, D:S.275, D:Q.277 Salt bridges: B:H.466 pi-Stacking: D:H.253, D:F.282, D:F.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Risal, D. et al., The Conformation of NAD Bound to Human Inosine Monophosphate Dehydrogenase Type II. To be Published

Release Date

2004-01-27

Peptides

Inosine-5'-monophosphate dehydrogenase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Inosine-5'-monophosphate dehydrogenase 2

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