SMTL ID : 4r7j.1

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase with the Internal Deletion Containing CBS Domain from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 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 19 PLIP interactions: 19 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:K.192, A:K.192, A:G.196, A:G.198, A:G.235, A:I.237, A:I.237, A:S.258, A:S.258, A:S.258 IMP.9: 22 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 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.173, B:S.199, 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:K.192, B:K.192, B:G.196, B:G.198, B:G.235, B:I.237, B:I.237, B:S.258, B:S.258, B:S.258 IMP.17: 22 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 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.173, 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:K.192, C:G.196, C:G.198, C:G.235, C:I.237, C:I.237, C:S.258, C:S.258, C:S.258 IMP.25: 22 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 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:N.173, D:S.199, 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:K.192, D:G.196, D:G.198, D:G.235, D:I.237, D:I.237, D:S.258, D:S.258, D:S.258

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

CL.2: 1 residues within 4Å: Chain A: H.57 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: H.57 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain C: H.57 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Chain D: H.57 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.164, P.165, N.166, L.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.164, A:N.166, A:L.167 GOL.11: 4 residues within 4Å: Chain B: Y.164, P.165, N.166, L.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.164, B:N.166, B:L.167 GOL.19: 4 residues within 4Å: Chain C: Y.164, P.165, N.166, L.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.164, C:N.166, C:L.167 GOL.27: 4 residues within 4Å: Chain D: Y.164, P.165, N.166, L.167 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.164, D:N.166, D:L.167

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

SO4.4: 3 residues within 4Å: Chain A: S.322, R.324 Chain C: K.307 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.322 Salt bridges: C:K.307 SO4.5: 2 residues within 4Å: Chain A: S.145, A.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.146 Salt bridges: A:K.74 SO4.6: 3 residues within 4Å: Chain A: I.78, Q.126, R.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.126 Water bridges: A:I.78 Salt bridges: A:R.129 SO4.12: 3 residues within 4Å: Chain B: S.322, R.324 Chain D: K.307 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Salt bridges: D:K.307 Hydrogen bonds: B:S.322 SO4.13: 2 residues within 4Å: Chain B: S.145, A.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.146 Salt bridges: B:K.74 SO4.14: 3 residues within 4Å: Chain B: I.78, Q.126, R.129 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.126 Water bridges: B:I.78 Salt bridges: B:R.129 SO4.20: 3 residues within 4Å: Chain B: K.307 Chain C: S.322, R.324 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.322 Salt bridges: B:K.307 SO4.21: 2 residues within 4Å: Chain C: S.145, A.146 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.146 Salt bridges: C:K.74 SO4.22: 3 residues within 4Å: Chain C: I.78, Q.126, R.129 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.126 Water bridges: C:I.78 Salt bridges: C:R.129 SO4.28: 3 residues within 4Å: Chain A: K.307 Chain D: S.322, R.324 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.322 Salt bridges: A:K.307 SO4.29: 2 residues within 4Å: Chain D: S.145, A.146 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.146 Salt bridges: D:K.74 SO4.30: 3 residues within 4Å: Chain D: I.78, Q.126, R.129 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.126 Water bridges: D:I.78 Salt bridges: D:R.129

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 3 residues within 4Å: Chain A: R.65, S.91, K.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.65, A:R.65, A:K.101, A:K.101 MPD.15: 3 residues within 4Å: Chain B: R.65, S.91, K.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.65, B:R.65, B:K.101, B:K.101 MPD.23: 3 residues within 4Å: Chain C: R.65, S.91, K.101 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.65, C:R.65, C:K.101, C:K.101 MPD.31: 3 residues within 4Å: Chain D: R.65, S.91, K.101 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.65, D:R.65, D:K.101, D:K.101

4 x K: POTASSIUM ION(Non-covalent)

K.8: 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: 2 interactions with chain D, 3 interactions with chain A Metal complexes: D:E.365, D:S.366, A:G.196, A:G.198, A:C.201 K.16: 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:E.365, C:S.366 K.24: 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:E.365, A:S.366 K.32: 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: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:G.196, D:G.198, D:C.201, B:E.365, B:S.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Inosine 5'-monophosphate Dehydrogenase with the Internal Deletion Containing CBS Domain from Campylobacter jejuni. To be Published (2014)

Release Date

2014-09-17

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Inosine-5'-monophosphate dehydrogenase

Related Entries With Identical Sequence