SMTL ID : 4myx.1 (1 other biounit)

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ame complexed with P32

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 21 residues within 4Å: Chain A: A.73, M.75, N.177, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, M.259, G.261, S.262, Y.285, G.287, M.288, G.289, E.313, G.314 Ligands: 2F0.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.177, A:S.203, A:D.238, A:G.240, A:G.261, A:S.262, A:Y.285, A:M.288, A:G.289, A:S.290, A:E.313 Water bridges: A:G.239 IMP.7: 23 residues within 4Å: Chain B: A.73, M.75, N.177, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, M.259, L.260, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 2F0.8 19 PLIP interactions: 1 interactions with chain A, 18 interactions with chain B Water bridges: A:H.371, B:G.202, B:G.239, B:G.239, B:I.241, B:S.262, B:S.262 Hydrogen bonds: B:N.177, B:S.203, B:D.238, B:G.240, B:I.241, B:G.261, B:S.262, B:Y.285, B:M.288, B:G.289, B:S.290, B:E.313 IMP.12: 23 residues within 4Å: Chain C: A.73, M.75, N.177, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, M.259, L.260, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 2F0.13 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.177, C:S.203, C:D.238, C:G.240, C:G.261, C:S.262, C:M.288, C:G.289, C:E.313 Water bridges: C:G.239, C:G.239, C:I.241, C:S.262, C:S.262, C:M.263 IMP.20: 24 residues within 4Å: Chain D: A.73, M.75, N.177, G.202, S.203, I.204, C.205, T.207, D.238, G.239, G.240, I.241, M.259, L.260, G.261, S.262, Y.285, G.287, M.288, G.289, S.290, E.313, G.314 Ligands: 2F0.17 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain D Water bridges: B:H.371, D:G.239, D:S.262 Hydrogen bonds: D:N.177, D:S.203, D:D.238, D:G.240, D:I.241, D:G.261, D:S.262, D:M.288, D:G.289, D:S.290, D:E.313

4 x 2F0: 2-chloro-5-{[(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)carbamoyl]amino}benzamide(Non-covalent)

2F0.2: 12 residues within 4Å: Chain A: A.150, H.151, T.207, M.288, G.289, M.294, V.311, E.313 Chain C: A.338, G.341, Y.342 Ligands: IMP.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.150, C:Y.342 Hydrogen bonds: A:T.207, A:E.313, A:E.313, A:E.313, C:Y.342 Water bridges: A:S.154, A:S.154 2F0.8: 15 residues within 4Å: Chain A: L.50, P.51, A.338, G.341, Y.342 Chain B: T.149, A.150, H.151, T.207, M.288, G.289, M.294, V.311, E.313 Ligands: IMP.7 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:P.51, A:Y.342, B:A.150, B:E.313 Hydrogen bonds: B:H.151, B:T.207, B:E.313, B:E.313, B:E.313 2F0.13: 14 residues within 4Å: Chain C: A.150, H.151, T.207, M.288, G.289, M.294, V.311, E.313 Chain D: L.50, P.51, A.338, G.341, Y.342 Ligands: IMP.12 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.338, D:Y.342, C:A.150, C:E.313 Hydrogen bonds: D:Y.342, C:H.151, C:T.207, C:E.313, C:E.313 2F0.17: 14 residues within 4Å: Chain B: L.50, P.51, A.338, G.341, Y.342 Chain D: A.150, H.151, T.207, M.288, G.289, M.294, V.311, E.313 Ligands: IMP.20 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:P.51, B:A.338, B:Y.342, D:A.150 Hydrogen bonds: D:T.207, D:E.313, D:E.313, D:E.313 Water bridges: D:S.154

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: R.208 Chain C: L.41, K.249, L.365, S.368, H.369 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.249, C:H.369 Water bridges: C:D.38 FMT.4: 3 residues within 4Å: Chain A: I.276, Q.278, G.279 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.278, A:G.279 FMT.10: 3 residues within 4Å: Chain B: T.180, A.181, D.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.181 FMT.11: 3 residues within 4Å: Chain A: G.34 Chain C: M.360, S.361 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.359 FMT.22: 8 residues within 4Å: Chain D: S.262, M.263, F.264, A.265, G.266, V.319, P.320, K.322 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.262, D:A.265, D:G.266 FMT.23: 5 residues within 4Å: Chain C: M.25 Chain D: A.45, C.343, N.354, A.355 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: V.373, Q.374, I.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.373, A:Q.374, A:I.375

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.6: 5 residues within 4Å: Chain A: A.181, E.182, K.185, E.227, K.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.227 Salt bridges: A:K.185, A:K.185, A:K.230

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 4 residues within 4Å: Chain A: S.361 Chain B: L.35, R.359, M.360 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.360 EDO.14: 7 residues within 4Å: Chain C: K.57, T.58, V.59, H.256, L.348, E.349, R.352 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.58, C:V.59, C:L.348, C:E.349, C:R.352 EDO.16: 7 residues within 4Å: Chain C: M.263, K.322, T.328, Q.331, L.332, P.380, N.381 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.322, C:K.322, C:N.381 EDO.18: 3 residues within 4Å: Chain C: F.30, V.31 Chain D: R.359 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.359, D:R.359, C:F.30 EDO.19: 4 residues within 4Å: Chain D: K.322, D.327, T.328, P.380 No protein-ligand interaction detected (PLIP) EDO.21: 2 residues within 4Å: Chain D: D.82, E.269 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 4 residues within 4Å: Chain C: R.229, K.230, H.231, G.232 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Bacillus anthracis str. Ame complexed with P32. To be Published

Release Date

2014-07-23

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inosine-5'-monophosphate dehydrogenase

Related Entries With Identical Sequence