SMTL ID : 5uwx.1

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P176

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x 8L7: N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-alpha-D-ribofuranosylamine(Non-covalent)

8L7.1: 18 residues within 4Å: Chain A: V.103, A.127, H.128, S.131, G.133, V.134, T.184, M.265, G.266, M.271, V.288, E.290 Chain B: L.27, P.28, S.315, G.318, Y.319 Ligands: IMP.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.127, A:E.290, B:P.28, B:Y.319 Hydrogen bonds: A:S.131, A:G.133, A:V.134, A:E.290, A:E.290 Water bridges: A:K.132, A:E.290, B:S.315 8L7.5: 13 residues within 4Å: Chain B: V.103, A.127, H.128, S.131, G.133, V.134, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.127 Hydrogen bonds: B:H.128, B:S.131, B:G.133, B:V.134, B:E.290, B:E.290 8L7.9: 14 residues within 4Å: Chain C: V.103, T.126, A.127, H.128, S.131, G.133, V.134, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.127 Hydrogen bonds: C:T.126, C:H.128, C:S.131, C:G.133, C:V.134, C:E.290, C:E.290 8L7.13: 14 residues within 4Å: Chain D: V.103, T.126, A.127, H.128, S.131, K.132, G.133, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.14 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.127 Hydrogen bonds: D:S.131, D:G.133, D:E.290, D:E.290 Water bridges: D:E.290

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.2: 23 residues within 4Å: Chain A: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8L7.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.154, A:S.180, A:D.215, A:G.217, A:G.238, A:S.239, A:Y.262, A:M.265, A:G.266, A:S.267, A:E.290 Water bridges: A:G.177, A:G.179, A:L.218, A:L.218, A:L.218, A:L.218 IMP.6: 23 residues within 4Å: Chain B: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8L7.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.154, B:S.180, B:D.215, B:G.217, B:G.238, B:S.239, B:Y.262, B:M.265, B:G.266, B:S.267, B:E.290 Water bridges: B:G.177, B:G.179, B:L.218, B:L.218, B:L.218, B:L.218 IMP.10: 23 residues within 4Å: Chain C: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8L7.9 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:N.154, C:S.180, C:D.215, C:G.217, C:G.238, C:S.239, C:Y.262, C:M.265, C:G.266, C:E.290 Water bridges: C:G.177, C:G.179, C:T.184, C:G.216, C:L.218, C:L.218 IMP.14: 23 residues within 4Å: Chain D: A.50, M.52, N.154, G.179, S.180, I.181, C.182, T.184, D.215, G.216, G.217, M.236, M.237, G.238, S.239, Y.262, G.264, M.265, G.266, S.267, E.290, G.291 Ligands: 8L7.13 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:N.154, D:S.180, D:D.215, D:G.217, D:G.238, D:S.239, D:M.265, D:G.266, D:S.267, D:E.290 Water bridges: D:G.177, D:G.179, D:G.216, D:L.218, D:I.240

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

MPD.3: 6 residues within 4Å: Chain A: K.9, A.156, T.157, P.158, D.200 Chain B: V.335 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.157, A:P.158, A:D.200, B:V.335 Hydrogen bonds: A:K.9, A:K.9 MPD.7: 5 residues within 4Å: Chain B: A.156, T.157, P.158, V.192, D.200 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.157, B:V.192 Hydrogen bonds: B:D.200 Water bridges: B:T.157 MPD.12: 5 residues within 4Å: Chain C: K.9, A.156, P.158, V.192, D.200 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.158, C:V.192, C:D.200 Hydrogen bonds: C:K.9, C:D.200 MPD.15: 4 residues within 4Å: Chain D: K.9, A.156, P.158, D.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.9, D:D.200

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 4 residues within 4Å: Chain A: K.219, Y.220, I.240, L.309 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.240, A:L.309 Hydrogen bonds: A:K.219 ACY.11: 1 residues within 4Å: Chain C: K.219 No protein-ligand interaction detected (PLIP) ACY.16: 1 residues within 4Å: Chain D: N.358 No protein-ligand interaction detected (PLIP)

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 7 residues within 4Å: Chain B: K.219, Y.220, I.240, Q.308, P.357, N.358, S.360 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.240, B:Q.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Inosine 5'-monophosphate Dehydrogenase fromClostridium perfringens Complexed with IMP and P176. To Be Published

Release Date

2017-03-01

Peptides

Inosine-5'-monophosphate dehydrogenase,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,Inosine-5'-monophosphate dehydrogenase

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