SMTL ID : 4mz1.2 (2 other biounits)

Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase, with a Internal Deletion of CBS Domain from Campylobacter jejuni complexed with inhibitor compound P12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 23 residues within 4Å: Chain A: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: 2F1.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.173, A:D.234, A:G.236, A:G.257, A:S.258, A:M.284, A:G.285, A:S.286, A:E.311 Water bridges: A:G.196, A:G.198, A:G.235, A:I.237, A:I.237, A:S.258 IMP.8: 23 residues within 4Å: Chain B: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: 2F1.9 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.173, B:D.234, B:G.236, B:G.257, B:S.258, B:M.284, B:G.285, B:S.286, B:E.311 Water bridges: B:G.196, B:G.198, B:G.235, B:I.237, B:I.237, B:S.258 IMP.15: 23 residues within 4Å: Chain C: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: 2F1.16 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:N.173, C:S.199, C:D.234, C:G.236, C:G.257, C:S.258, C:M.284, C:G.285, C:S.286, C:E.311 Water bridges: C:G.196, C:G.198, C:G.235, C:I.237, C:I.237, C:S.258 IMP.22: 23 residues within 4Å: Chain D: A.49, M.51, N.173, G.198, S.199, I.200, C.201, T.203, D.234, G.235, G.236, M.255, I.256, G.257, S.258, Y.281, G.283, M.284, G.285, S.286, E.311, G.312 Ligands: 2F1.23 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:N.173, D:D.234, D:G.236, D:G.257, D:S.258, D:M.284, D:G.285, D:S.286, D:E.311 Water bridges: D:G.196, D:G.198, D:G.235, D:I.237, D:I.237, D:S.258

4 x 2F1: 1-(4-bromophenyl)-3-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea(Non-covalent)

2F1.2: 14 residues within 4Å: Chain A: A.146, H.147, T.203, M.284, G.285, M.290, V.309, E.311 Chain D: V.25, P.27, S.336, G.339, Y.340 Ligands: IMP.1 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:P.27, D:Y.340, A:A.146, A:E.311 Halogen bonds: D:V.25 Hydrogen bonds: A:E.311, A:E.311 Water bridges: A:A.146 2F1.9: 14 residues within 4Å: Chain B: A.146, H.147, T.203, M.284, G.285, M.290, V.309, E.311 Chain C: V.25, P.27, S.336, G.339, Y.340 Ligands: IMP.8 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:P.27, C:Y.340, B:A.146, B:E.311 Halogen bonds: C:V.25 Hydrogen bonds: B:E.311, B:E.311 Water bridges: B:A.146 2F1.16: 14 residues within 4Å: Chain A: V.25, P.27, S.336, G.339, Y.340 Chain C: A.146, H.147, T.203, M.284, G.285, M.290, V.309, E.311 Ligands: IMP.15 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:A.146, C:E.311, A:P.27, A:Y.340 Hydrogen bonds: C:E.311, C:E.311 Water bridges: C:A.146 Halogen bonds: A:V.25 2F1.23: 14 residues within 4Å: Chain B: V.25, P.27, S.336, G.339, Y.340 Chain D: A.146, H.147, T.203, M.284, G.285, M.290, V.309, E.311 Ligands: IMP.22 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:P.27, B:Y.340, D:A.146, D:E.311 Halogen bonds: B:V.25 Hydrogen bonds: D:E.311, D:E.311 Water bridges: D:A.146

4 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: G.196, P.197, G.198, C.201 Chain D: E.365, S.366, H.367, H.369 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Metal complexes: A:G.196, A:G.198, A:C.201, D:S.366, D:H.367 K.10: 8 residues within 4Å: Chain B: G.196, P.197, G.198, C.201 Chain C: E.365, S.366, H.367, H.369 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:G.196, B:G.198, B:C.201, C:S.366, C:H.367 K.17: 8 residues within 4Å: Chain A: E.365, S.366, H.367, H.369 Chain C: G.196, P.197, G.198, C.201 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:G.196, C:G.198, C:C.201, A:S.366, A:H.367 K.24: 8 residues within 4Å: Chain B: E.365, S.366, H.367, H.369 Chain D: G.196, P.197, G.198, C.201 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Metal complexes: B:S.366, B:H.367, D:G.196, D:G.198, D:C.201

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: R.276, Y.278, R.316 Chain D: T.372 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.278, D:T.372 Salt bridges: A:R.316 PO4.7: 3 residues within 4Å: Chain A: I.78, Q.126, R.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.126 Salt bridges: A:R.129 PO4.11: 4 residues within 4Å: Chain B: R.276, Y.278, R.316 Chain C: T.372 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.372, B:Y.278 Salt bridges: B:R.316 PO4.14: 3 residues within 4Å: Chain B: I.78, Q.126, R.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.126 Salt bridges: B:R.129 PO4.18: 4 residues within 4Å: Chain A: T.372 Chain C: R.276, Y.278, R.316 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.372, C:Y.278 Salt bridges: C:R.316 PO4.21: 3 residues within 4Å: Chain C: I.78, Q.126, R.129 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.126 Salt bridges: C:R.129 PO4.25: 4 residues within 4Å: Chain B: T.372 Chain D: R.276, Y.278, R.316 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Y.278, B:T.372 Salt bridges: D:R.316 PO4.28: 3 residues within 4Å: Chain D: I.78, Q.126, R.129 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.126 Salt bridges: D:R.129

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

SO4.5: 1 residues within 4Å: Chain A: R.65 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.65 SO4.6: 1 residues within 4Å: Chain A: H.57 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.57 SO4.12: 1 residues within 4Å: Chain B: R.65 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.65 SO4.13: 1 residues within 4Å: Chain B: H.57 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.57 SO4.19: 1 residues within 4Å: Chain C: R.65 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.65 SO4.20: 1 residues within 4Å: Chain C: H.57 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.57 SO4.26: 1 residues within 4Å: Chain D: R.65 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.65 SO4.27: 1 residues within 4Å: Chain D: H.57 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.57

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 Campylobacter jejuni complexed with inhibitor compound P12. To be Published (2013)

Release Date

2014-01-01

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Inosine-5'-monophosphate dehydrogenase

Related Entries With Identical Sequence