SMTL ID : 1nf7.2 (1 other biounit)

Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with Ribavirin Monophosphate and C2-Mycophenolic Adenine Dinucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: G.326, S.327, G.328, C.331 Chain C: E.500, G.501, G.502 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:E.500, C:G.502, A:G.328, A:C.331 K.15: 7 residues within 4Å: Chain B: G.326, S.327, G.328, C.331 Chain D: E.500, G.501, G.502 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:G.328, B:C.331, D:E.500, D:G.502 K.29: 7 residues within 4Å: Chain B: E.500, G.501, G.502 Chain C: G.326, S.327, G.328, C.331 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Metal complexes: B:E.500, B:G.502, C:G.328, C:C.331 K.43: 7 residues within 4Å: Chain A: E.500, G.501, G.502 Chain D: G.326, S.327, G.328, C.331 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.328, D:C.331, A:E.500, A:G.502

4 x RVP: RIBAVIRIN MONOPHOSPHATE(Non-covalent)

RVP.2: 24 residues within 4Å: Chain A: S.68, M.70, N.303, R.322, S.327, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, M.386, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: MYD.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.68, A:S.68, A:N.303, A:R.322, A:S.329, A:G.366, A:G.387, A:S.388, A:S.388, A:Y.411, A:M.414, A:G.415, A:Q.441 Water bridges: A:I.367, A:I.367, A:I.367, A:S.388, A:S.388 RVP.16: 24 residues within 4Å: Chain B: S.68, M.70, N.303, R.322, S.327, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, M.386, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: MYD.17 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.68, B:S.68, B:N.303, B:R.322, B:S.329, B:G.366, B:G.387, B:S.388, B:S.388, B:Y.411, B:M.414, B:G.415, B:Q.441 Water bridges: B:I.367, B:I.367, B:I.367, B:S.388, B:S.388 RVP.30: 24 residues within 4Å: Chain C: S.68, M.70, N.303, R.322, S.327, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, M.386, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: MYD.31 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:S.68, C:S.68, C:N.303, C:R.322, C:S.329, C:G.366, C:G.387, C:S.388, C:S.388, C:Y.411, C:M.414, C:G.415, C:Q.441 Water bridges: C:I.367, C:I.367, C:I.367, C:S.388, C:S.388 RVP.44: 24 residues within 4Å: Chain D: S.68, M.70, N.303, R.322, S.327, G.328, S.329, I.330, C.331, D.364, G.365, G.366, M.385, M.386, G.387, S.388, Y.411, G.413, M.414, G.415, S.416, Q.441, G.442 Ligands: MYD.45 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:S.68, D:S.68, D:N.303, D:R.322, D:S.329, D:G.366, D:G.387, D:S.388, D:S.388, D:Y.411, D:M.414, D:G.415, D:Q.441 Water bridges: D:I.367, D:I.367, D:I.367, D:S.388, D:S.388

4 x MYD: {[5-(6-AMINO-PURIN-7-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-[2-(4-HYDROXY-6-METHOXY-7-METHYL-3-OXO-1,3-DIHYDRO-ISOBENZOFURAN-5-YL)-ETHYL] ESTER(Non-covalent)

MYD.3: 17 residues within 4Å: Chain A: T.252, D.274, S.275, S.276, F.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, G.415, Q.441 Chain C: T.45, Q.469 Ligands: RVP.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.252, A:D.274, A:S.276, A:G.326, A:T.333, A:T.333, A:Q.441, C:Q.469 Water bridges: A:S.276, A:R.322 pi-Stacking: A:H.253, A:H.253, A:F.282, A:F.282 MYD.17: 17 residues within 4Å: Chain B: T.252, D.274, S.275, S.276, F.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, G.415, Q.441 Chain D: T.45, Q.469 Ligands: RVP.16 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.252, B:D.274, B:S.276, B:G.326, B:T.333, B:T.333, B:Q.441, D:Q.469 Water bridges: B:S.276, B:R.322 pi-Stacking: B:H.253, B:H.253, B:F.282, B:F.282 MYD.31: 17 residues within 4Å: Chain B: T.45, Q.469 Chain C: T.252, D.274, S.275, S.276, F.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, G.415, Q.441 Ligands: RVP.30 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.252, C:D.274, C:S.276, C:G.326, C:T.333, C:T.333, C:Q.441, B:Q.469 Water bridges: C:S.276, C:R.322 pi-Stacking: C:H.253, C:H.253, C:F.282, C:F.282 MYD.45: 17 residues within 4Å: Chain A: T.45, Q.469 Chain D: T.252, D.274, S.275, S.276, F.282, N.303, R.322, G.324, M.325, G.326, C.331, T.333, G.415, Q.441 Ligands: RVP.44 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.252, D:D.274, D:S.276, D:G.326, D:T.333, D:T.333, D:Q.441, A:Q.469 Water bridges: D:S.276, D:R.322 pi-Stacking: D:H.253, D:H.253, D:F.282, D:F.282

44 x UNK: UNKNOWN(Non-functional Binders)

UNK.4: 2 residues within 4Å: Chain A: M.420 Ligands: UNK.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.420 UNK.5: 3 residues within 4Å: Chain A: K.438 Ligands: UNK.4, UNK.6 No protein-ligand interaction detected (PLIP) UNK.6: 3 residues within 4Å: Chain A: K.438 Ligands: UNK.5, UNK.7 No protein-ligand interaction detected (PLIP) UNK.7: 2 residues within 4Å: Ligands: UNK.6, UNK.8 No protein-ligand interaction detected (PLIP) UNK.8: 2 residues within 4Å: Ligands: UNK.7, UNK.9 No protein-ligand interaction detected (PLIP) UNK.9: 1 residues within 4Å: Ligands: UNK.8 No protein-ligand interaction detected (PLIP) UNK.10: 1 residues within 4Å: Ligands: UNK.11 No protein-ligand interaction detected (PLIP) UNK.11: 2 residues within 4Å: Ligands: UNK.10, UNK.12 No protein-ligand interaction detected (PLIP) UNK.12: 2 residues within 4Å: Ligands: UNK.11, UNK.13 No protein-ligand interaction detected (PLIP) UNK.13: 2 residues within 4Å: Ligands: UNK.12, UNK.14 No protein-ligand interaction detected (PLIP) UNK.14: 3 residues within 4Å: Chain A: I.437 Chain C: P.458 Ligands: UNK.13 No protein-ligand interaction detected (PLIP) UNK.18: 2 residues within 4Å: Chain B: M.420 Ligands: UNK.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.420 UNK.19: 3 residues within 4Å: Chain B: K.438 Ligands: UNK.18, UNK.20 No protein-ligand interaction detected (PLIP) UNK.20: 3 residues within 4Å: Chain B: K.438 Ligands: UNK.19, UNK.21 No protein-ligand interaction detected (PLIP) UNK.21: 2 residues within 4Å: Ligands: UNK.20, UNK.22 No protein-ligand interaction detected (PLIP) UNK.22: 2 residues within 4Å: Ligands: UNK.21, UNK.23 No protein-ligand interaction detected (PLIP) UNK.23: 1 residues within 4Å: Ligands: UNK.22 No protein-ligand interaction detected (PLIP) UNK.24: 1 residues within 4Å: Ligands: UNK.25 No protein-ligand interaction detected (PLIP) UNK.25: 2 residues within 4Å: Ligands: UNK.24, UNK.26 No protein-ligand interaction detected (PLIP) UNK.26: 2 residues within 4Å: Ligands: UNK.25, UNK.27 No protein-ligand interaction detected (PLIP) UNK.27: 2 residues within 4Å: Ligands: UNK.26, UNK.28 No protein-ligand interaction detected (PLIP) UNK.28: 3 residues within 4Å: Chain B: I.437 Chain D: P.458 Ligands: UNK.27 No protein-ligand interaction detected (PLIP) UNK.32: 2 residues within 4Å: Chain C: M.420 Ligands: UNK.33 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:M.420 UNK.33: 3 residues within 4Å: Chain C: K.438 Ligands: UNK.32, UNK.34 No protein-ligand interaction detected (PLIP) UNK.34: 3 residues within 4Å: Chain C: K.438 Ligands: UNK.33, UNK.35 No protein-ligand interaction detected (PLIP) UNK.35: 2 residues within 4Å: Ligands: UNK.34, UNK.36 No protein-ligand interaction detected (PLIP) UNK.36: 2 residues within 4Å: Ligands: UNK.35, UNK.37 No protein-ligand interaction detected (PLIP) UNK.37: 1 residues within 4Å: Ligands: UNK.36 No protein-ligand interaction detected (PLIP) UNK.38: 1 residues within 4Å: Ligands: UNK.39 No protein-ligand interaction detected (PLIP) UNK.39: 2 residues within 4Å: Ligands: UNK.38, UNK.40 No protein-ligand interaction detected (PLIP) UNK.40: 2 residues within 4Å: Ligands: UNK.39, UNK.41 No protein-ligand interaction detected (PLIP) UNK.41: 2 residues within 4Å: Ligands: UNK.40, UNK.42 No protein-ligand interaction detected (PLIP) UNK.42: 3 residues within 4Å: Chain B: P.458 Chain C: I.437 Ligands: UNK.41 No protein-ligand interaction detected (PLIP) UNK.46: 2 residues within 4Å: Chain D: M.420 Ligands: UNK.47 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:M.420 UNK.47: 3 residues within 4Å: Chain D: K.438 Ligands: UNK.46, UNK.48 No protein-ligand interaction detected (PLIP) UNK.48: 3 residues within 4Å: Chain D: K.438 Ligands: UNK.47, UNK.49 No protein-ligand interaction detected (PLIP) UNK.49: 2 residues within 4Å: Ligands: UNK.48, UNK.50 No protein-ligand interaction detected (PLIP) UNK.50: 2 residues within 4Å: Ligands: UNK.49, UNK.51 No protein-ligand interaction detected (PLIP) UNK.51: 1 residues within 4Å: Ligands: UNK.50 No protein-ligand interaction detected (PLIP) UNK.52: 1 residues within 4Å: Ligands: UNK.53 No protein-ligand interaction detected (PLIP) UNK.53: 2 residues within 4Å: Ligands: UNK.52, UNK.54 No protein-ligand interaction detected (PLIP) UNK.54: 2 residues within 4Å: Ligands: UNK.53, UNK.55 No protein-ligand interaction detected (PLIP) UNK.55: 2 residues within 4Å: Ligands: UNK.54, UNK.56 No protein-ligand interaction detected (PLIP) UNK.56: 3 residues within 4Å: Chain A: P.458 Chain D: I.437 Ligands: UNK.55 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Risal, D. et al., Crystal Structure of Human Inosine Monophosphate Dehydrogenase type II complexed with the MPA/NAD analog C2-MAD. 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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