SMTL ID : 5uzc.2 (1 other biounit)

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-octamer

Ligands

8 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 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: 8N1.2 15 PLIP interactions: 15 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 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: 8N1.7 15 PLIP interactions: 15 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:E.290 Water bridges: B:G.177, B:G.179, 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: 8N1.11 13 PLIP interactions: 13 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:M.265, C:G.266, C:S.267, C:E.290 Water bridges: C:G.177, C:G.179, C:G.216 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: 8N1.15 14 PLIP interactions: 14 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:E.290 Water bridges: D:G.177, D:G.179, D:G.216, D:L.218, D:L.218 IMP.18: 23 residues within 4Å: Chain E: 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: 8N1.19 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:N.154, E:S.180, E:D.215, E:G.217, E:G.238, E:S.239, E:M.265, E:G.266, E:S.267, E:E.290 Water bridges: E:G.177, E:G.179, E:T.184, E:L.218, E:L.218 IMP.23: 23 residues within 4Å: Chain F: 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: 8N1.24 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:N.154, F:S.180, F:D.215, F:G.217, F:G.238, F:S.239, F:M.265, F:G.266, F:E.290 Water bridges: F:G.177, F:G.179, F:T.184, F:L.218, F:L.218, F:L.218 IMP.27: 23 residues within 4Å: Chain G: 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: 8N1.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:N.154, G:S.180, G:D.215, G:G.217, G:G.238, G:S.239, G:Y.262, G:M.265, G:G.266, G:S.267, G:E.290 Water bridges: G:G.177, G:G.179, G:T.184, G:G.216 IMP.31: 23 residues within 4Å: Chain H: 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: 8N1.32 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:N.154, H:S.180, H:D.215, H:G.217, H:G.238, H:S.239, H:Y.262, H:M.265, H:G.266, H:E.290 Water bridges: H:G.177, H:G.179, H:T.184, H:G.216, H:L.218, H:L.218

8 x 8N1: N-{2-chloro-5-[({2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}carbamoyl)amino]phenyl}-beta-D-xylofuranosylamine(Non-covalent)

8N1.2: 20 residues within 4Å: Chain A: 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 Chain D: V.26, L.27, P.28, S.315, G.318, Y.319 Ligands: IMP.1 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:A.127, D:P.28, D:Y.319, D:Y.319 Hydrogen bonds: A:A.127, A:H.128, A:S.131, A:S.131, A:G.133, A:V.134, A:E.290, A:E.290, D:Y.319 Water bridges: A:K.132, D:S.315, D:S.315 Halogen bonds: D:V.26 8N1.7: 16 residues within 4Å: Chain A: L.27, P.28, S.315, G.318, Y.319 Chain B: T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.6 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.127, A:P.28, A:Y.319 Hydrogen bonds: B:A.127, B:H.128, B:S.131, B:E.290, B:E.290 Water bridges: B:S.131, B:E.290, A:S.315 8N1.11: 17 residues within 4Å: Chain B: V.26, L.27, P.28, S.315, G.318, Y.319 Chain C: T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.10 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.127, C:E.290, B:P.28, B:Y.319 Hydrogen bonds: C:A.127, C:H.128, C:H.128, C:S.131, C:E.290, C:E.290 Water bridges: C:S.131, B:S.315 8N1.15: 20 residues within 4Å: Chain C: V.26, L.27, P.28, S.315, G.318, Y.319 Chain D: 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.14 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:P.28, C:Y.319, C:Y.319, D:A.127 Hydrogen bonds: C:Y.319, D:A.127, D:H.128, D:S.131, D:G.133, D:V.134, D:E.290, D:E.290 Water bridges: C:S.315, C:S.315, D:K.132 8N1.19: 20 residues within 4Å: Chain E: 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 Chain H: V.26, L.27, P.28, S.315, G.318, Y.319 Ligands: IMP.18 17 PLIP interactions: 12 interactions with chain E, 5 interactions with chain H Hydrophobic interactions: E:A.127, H:P.28, H:Y.319, H:Y.319 Hydrogen bonds: E:T.126, E:A.127, E:H.128, E:S.131, E:S.131, E:G.133, E:V.134, E:E.290, E:E.290 Water bridges: E:K.132, E:E.290, H:S.315 Halogen bonds: H:V.26 8N1.24: 16 residues within 4Å: Chain E: L.27, P.28, S.315, G.318, Y.319 Chain F: T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.23 12 PLIP interactions: 8 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:A.127, E:P.28, E:Y.319 Hydrogen bonds: F:T.126, F:A.127, F:H.128, F:S.131, F:E.290, F:E.290 Water bridges: F:S.131, E:S.315, E:S.315 8N1.28: 17 residues within 4Å: Chain F: V.26, L.27, P.28, S.315, G.318, Y.319 Chain G: T.126, A.127, H.128, S.131, T.184, M.265, G.266, M.271, V.288, E.290 Ligands: IMP.27 12 PLIP interactions: 3 interactions with chain F, 9 interactions with chain G Hydrophobic interactions: F:P.28, F:Y.319, G:A.127, G:E.290 Water bridges: F:S.315, G:S.131 Hydrogen bonds: G:A.127, G:H.128, G:H.128, G:S.131, G:E.290, G:E.290 8N1.32: 20 residues within 4Å: Chain G: V.26, L.27, P.28, S.315, G.318, Y.319 Chain H: 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.31 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain G Hydrophobic interactions: H:A.127, G:P.28, G:Y.319, G:Y.319 Hydrogen bonds: H:A.127, H:H.128, H:S.131, H:G.133, H:V.134, H:E.290, H:E.290 Water bridges: H:K.132, H:E.290, G:S.315

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

MPD.3: 7 residues within 4Å: Chain A: L.8, K.9, A.156, T.157, P.158, D.200 Chain D: V.20 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.20, A:T.157 Hydrogen bonds: A:D.200 MPD.8: 6 residues within 4Å: Chain A: V.20 Chain B: K.9, A.156, P.158, V.192, D.200 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.192, B:D.200, A:V.20 Hydrogen bonds: B:D.200 Water bridges: B:T.157 MPD.16: 6 residues within 4Å: Chain C: V.335 Chain D: L.8, K.9, A.156, P.158, D.200 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.158, C:V.335 Hydrogen bonds: D:K.9, D:D.200 MPD.20: 7 residues within 4Å: Chain E: L.8, K.9, A.156, T.157, P.158, D.200 Chain H: V.20 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:T.157, H:V.20 Hydrogen bonds: E:D.200, E:D.200 MPD.25: 6 residues within 4Å: Chain E: V.20 Chain F: K.9, A.156, P.158, V.192, D.200 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:V.20, F:V.192, F:D.200 Hydrogen bonds: F:D.200, F:D.200 Water bridges: F:T.157 MPD.33: 6 residues within 4Å: Chain G: V.335 Chain H: L.8, K.9, A.156, P.158, D.200 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:P.158, G:V.335 Hydrogen bonds: H:K.9, H:D.200, H:D.200

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

ACY.4: 2 residues within 4Å: Chain A: K.219, K.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.219 Salt bridges: A:K.299 ACY.13: 1 residues within 4Å: Chain C: K.219 No protein-ligand interaction detected (PLIP) ACY.17: 2 residues within 4Å: Chain D: K.219, N.358 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.221 ACY.21: 2 residues within 4Å: Chain E: K.219, K.299 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.219 Salt bridges: E:K.299 ACY.30: 1 residues within 4Å: Chain G: K.219 1 PLIP interactions: 1 interactions with chain G Water bridges: G:T.305 ACY.34: 2 residues within 4Å: Chain H: K.219, N.358 1 PLIP interactions: 1 interactions with chain H Water bridges: H:S.221

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

FMT.5: 4 residues within 4Å: Chain A: S.339 Chain B: S.339 Chain C: S.339 Chain D: S.339 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:S.339, A:S.339, C:S.339, B:S.339 FMT.9: 1 residues within 4Å: Chain B: K.219 No protein-ligand interaction detected (PLIP) FMT.22: 4 residues within 4Å: Chain E: S.339 Chain F: S.339 Chain G: S.339 Chain H: S.339 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: E:S.339, F:S.339, G:S.339, H:S.339 FMT.26: 1 residues within 4Å: Chain F: K.219 No protein-ligand interaction detected (PLIP)

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

MRD.12: 5 residues within 4Å: Chain B: V.335 Chain C: K.9, A.156, P.158, D.200 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.9, C:D.200, C:D.200 Hydrophobic interactions: B:V.335 MRD.29: 5 residues within 4Å: Chain F: V.335 Chain G: K.9, A.156, P.158, D.200 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:K.9, G:D.200 Hydrophobic interactions: F:V.335

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 P221. To Be Published

Release Date

2017-03-22

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Inosine-5'-monophosphate dehydrogenase

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