SMTL ID : 7oj1.1

Bacillus subtilis IMPDH in complex with Ap4A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-4-4-mer

Ligands

8 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.1: 26 residues within 4Å: Chain A: I.94, P.97, F.98, I.117, S.118, G.119, P.121, I.129, T.131, N.132, R.133, D.134, T.147, E.150, L.151, V.152, I.172, E.173, K.174, L.180, T.182, I.183, K.184, D.185 Chain F: R.141 Ligands: MG.2 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:F.98, A:S.118, A:S.118, A:G.119, A:G.119, A:T.131, A:N.132, A:R.133, A:R.133, A:D.134, A:V.152, A:E.173, A:T.182, A:K.184, A:D.185, A:K.188, F:R.141 Salt bridges: A:K.174, A:K.174, A:K.174, A:K.174, A:K.184, F:R.141 B4P.3: 26 residues within 4Å: Chain B: I.94, P.97, F.98, I.117, S.118, G.119, P.121, I.129, T.131, N.132, R.133, D.134, T.147, E.150, L.151, V.152, I.172, E.173, K.174, L.180, T.182, I.183, K.184, D.185 Chain E: R.141 Ligands: MG.4 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:F.98, B:S.118, B:S.118, B:G.119, B:G.119, B:T.131, B:N.132, B:R.133, B:R.133, B:D.134, B:V.152, B:E.173, B:T.182, B:K.184, B:D.185, B:K.188, E:R.141 Salt bridges: B:K.174, B:K.174, B:K.174, B:K.174, B:K.184, E:R.141 B4P.5: 26 residues within 4Å: Chain C: I.94, P.97, F.98, I.117, S.118, G.119, P.121, I.129, T.131, N.132, R.133, D.134, T.147, E.150, L.151, V.152, I.172, E.173, K.174, L.180, T.182, I.183, K.184, D.185 Chain H: R.141 Ligands: MG.6 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:F.98, C:S.118, C:S.118, C:G.119, C:G.119, C:T.131, C:N.132, C:R.133, C:R.133, C:D.134, C:V.152, C:E.173, C:T.182, C:K.184, C:D.185, C:K.188, H:R.141 Salt bridges: C:K.174, C:K.174, C:K.174, C:K.174, C:K.184, H:R.141 B4P.7: 26 residues within 4Å: Chain D: I.94, P.97, F.98, I.117, S.118, G.119, P.121, I.129, T.131, N.132, R.133, D.134, T.147, E.150, L.151, V.152, I.172, E.173, K.174, L.180, T.182, I.183, K.184, D.185 Chain G: R.141 Ligands: MG.8 23 PLIP interactions: 2 interactions with chain G, 21 interactions with chain D Hydrogen bonds: G:R.141, D:F.98, D:S.118, D:S.118, D:G.119, D:G.119, D:T.131, D:N.132, D:R.133, D:R.133, D:D.134, D:V.152, D:E.173, D:T.182, D:K.184, D:D.185, D:K.188 Salt bridges: G:R.141, D:K.174, D:K.174, D:K.174, D:K.174, D:K.184 B4P.9: 27 residues within 4Å: Chain B: R.133 Chain E: I.96, P.99, F.100, I.120, S.121, G.122, P.124, I.137, T.139, N.140, R.141, D.142, T.158, E.161, L.162, V.163, I.183, E.184, K.185, P.187, L.198, T.200, I.201, K.202, D.203 Ligands: MG.10 22 PLIP interactions: 20 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:F.100, E:S.121, E:S.121, E:G.122, E:T.139, E:N.140, E:R.141, E:D.142, E:T.158, E:V.163, E:E.184, E:E.184, E:K.185, E:K.185, E:K.202, E:D.203, B:R.133, B:R.133 Salt bridges: E:K.185, E:K.185, E:K.185, E:K.185 B4P.11: 27 residues within 4Å: Chain A: R.133 Chain F: I.96, P.99, F.100, I.120, S.121, G.122, P.124, I.137, T.139, N.140, R.141, D.142, T.158, E.161, L.162, V.163, I.183, E.184, K.185, P.187, L.198, T.200, I.201, K.202, D.203 Ligands: MG.12 22 PLIP interactions: 20 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:F.100, F:S.121, F:S.121, F:G.122, F:T.139, F:N.140, F:R.141, F:D.142, F:T.158, F:V.163, F:E.184, F:E.184, F:K.185, F:K.185, F:K.202, F:D.203, A:R.133, A:R.133 Salt bridges: F:K.185, F:K.185, F:K.185, F:K.185 B4P.13: 27 residues within 4Å: Chain D: R.133 Chain G: I.96, P.99, F.100, I.120, S.121, G.122, P.124, I.137, T.139, N.140, R.141, D.142, T.158, E.161, L.162, V.163, I.183, E.184, K.185, P.187, L.198, T.200, I.201, K.202, D.203 Ligands: MG.14 22 PLIP interactions: 20 interactions with chain G, 2 interactions with chain D Hydrogen bonds: G:F.100, G:S.121, G:S.121, G:G.122, G:T.139, G:N.140, G:R.141, G:D.142, G:T.158, G:V.163, G:E.184, G:E.184, G:K.185, G:K.185, G:K.202, G:D.203, D:R.133, D:R.133 Salt bridges: G:K.185, G:K.185, G:K.185, G:K.185 B4P.15: 27 residues within 4Å: Chain C: R.133 Chain H: I.96, P.99, F.100, I.120, S.121, G.122, P.124, I.137, T.139, N.140, R.141, D.142, T.158, E.161, L.162, V.163, I.183, E.184, K.185, P.187, L.198, T.200, I.201, K.202, D.203 Ligands: MG.16 22 PLIP interactions: 20 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:F.100, H:S.121, H:S.121, H:G.122, H:T.139, H:N.140, H:R.141, H:D.142, H:T.158, H:V.163, H:E.184, H:E.184, H:K.185, H:K.185, H:K.202, H:D.203, C:R.133, C:R.133 Salt bridges: H:K.185, H:K.185, H:K.185, H:K.185

8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: B4P.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: B4P.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: B4P.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: B4P.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: R.133 Ligands: B4P.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: R.133 Ligands: B4P.11 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: R.133 Ligands: B4P.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain C: R.133 Ligands: B4P.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giammarinaro, P.I. et al., Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis. Nat Microbiol (2022)

Release Date

2022-09-14

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD
Inosine-5'-monophosphate dehydrogenase: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
B

F
B

G
B

H
B

Inosine-5'-monophosphate dehydrogenase

Inosine-5'-monophosphate dehydrogenase