SMTL ID : 7pmz.1 (1 other biounit)

Crystal structure of Streptomyces coelicolor guaB (IMP dehydrogenase) bound to ATP and ppGpp at 2.0 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-octamer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 23 residues within 4Å: Chain A: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Chain G: R.148, K.189, E.191 Ligands: G4P.2, MG.3, MG.4, ATP.25, MG.28 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain G Hydrogen bonds: A:S.130, A:T.146, A:R.148, A:D.149, A:T.165, A:T.165, A:V.170, A:V.170, A:E.191, A:K.192 Water bridges: A:N.147, A:N.147, A:N.147 Salt bridges: A:R.148, A:K.192, A:K.192, G:R.148, G:R.148, G:R.148 ATP.5: 23 residues within 4Å: Chain B: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Chain H: R.148, K.189, E.191 Ligands: G4P.6, MG.7, MG.8, ATP.29, MG.32 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain H Hydrogen bonds: B:S.130, B:S.130, B:T.146, B:R.148, B:D.149, B:T.165, B:T.165, B:V.170, B:V.170, B:E.191, B:K.192, H:K.189, H:E.191 Water bridges: B:N.147, B:N.147, B:R.148 Salt bridges: B:R.148, B:R.148, B:K.192, B:K.192, H:R.148, H:R.148, H:R.148 ATP.9: 23 residues within 4Å: Chain C: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Chain D: R.148, K.189, E.191 Ligands: G4P.10, MG.11, MG.12, ATP.13, MG.15 19 PLIP interactions: 4 interactions with chain D, 15 interactions with chain C Hydrogen bonds: D:E.191, C:S.130, C:T.146, C:R.148, C:D.149, C:T.165, C:T.165, C:V.170, C:V.170, C:E.191, C:K.192 Salt bridges: D:R.148, D:R.148, D:R.148, C:R.148, C:K.192, C:K.192 Water bridges: C:N.147, C:R.148 ATP.13: 23 residues within 4Å: Chain C: R.148, K.189, E.191 Chain D: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Ligands: ATP.9, MG.12, G4P.14, MG.15, MG.16 21 PLIP interactions: 17 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.130, D:I.144, D:T.146, D:R.148, D:T.165, D:T.165, D:V.170, D:V.170, D:E.191, D:K.192, C:K.189 Water bridges: D:N.147, D:N.147, D:N.147, D:R.148 Salt bridges: D:R.148, D:K.192, D:K.192, C:R.148, C:R.148, C:R.148 ATP.17: 23 residues within 4Å: Chain E: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Chain F: R.148, K.189, E.191 Ligands: G4P.18, MG.19, MG.20, ATP.21, MG.24 19 PLIP interactions: 15 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:S.130, E:T.146, E:T.146, E:R.148, E:T.165, E:T.165, E:V.170, E:V.170, E:E.191 Water bridges: E:S.130, E:N.147, E:N.147, F:E.191 Salt bridges: E:R.148, E:K.192, E:K.192, F:R.148, F:R.148, F:R.148 ATP.21: 23 residues within 4Å: Chain E: R.148, K.189, E.191 Chain F: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Ligands: ATP.17, MG.19, G4P.22, MG.23, MG.24 21 PLIP interactions: 18 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:S.130, F:S.130, F:I.144, F:T.146, F:R.148, F:T.165, F:T.165, F:V.170, F:V.170, F:E.191, F:K.192 Water bridges: F:N.147, F:N.147, F:N.147, F:R.148 Salt bridges: F:R.148, F:K.192, F:K.192, E:R.148, E:R.148, E:R.148 ATP.25: 23 residues within 4Å: Chain A: R.148, K.189, E.191 Chain G: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Ligands: ATP.1, MG.4, G4P.26, MG.27, MG.28 21 PLIP interactions: 17 interactions with chain G, 4 interactions with chain A Hydrogen bonds: G:S.130, G:S.130, G:T.146, G:R.148, G:D.149, G:T.165, G:T.165, G:V.170, G:V.170, G:E.191, G:K.192, A:E.191 Water bridges: G:N.147, G:N.147, G:R.148 Salt bridges: G:R.148, G:K.192, G:K.192, A:R.148, A:R.148, A:R.148 ATP.29: 23 residues within 4Å: Chain B: R.148, K.189, E.191 Chain H: S.130, I.144, V.145, T.146, N.147, R.148, D.149, T.165, L.169, V.170, I.190, E.191, K.192, L.193, P.194 Ligands: ATP.5, MG.8, G4P.30, MG.31, MG.32 20 PLIP interactions: 16 interactions with chain H, 4 interactions with chain B Hydrogen bonds: H:I.144, H:T.146, H:N.147, H:R.148, H:T.165, H:T.165, H:V.170, H:V.170, H:E.191, H:K.192 Water bridges: H:S.130, H:N.147, B:E.191 Salt bridges: H:R.148, H:R.148, H:K.192, H:K.192, B:R.148, B:R.148, B:R.148

8 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.2: 16 residues within 4Å: Chain A: R.74, D.121, C.124, A.125, R.128, I.129, S.130, N.147, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.1, MG.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.130, A:S.130, A:N.147, A:N.147 Water bridges: A:R.128, A:R.128, A:S.130, A:S.130, A:K.192, A:K.209 Salt bridges: A:R.74, A:D.121, A:R.128, A:R.128, A:K.192, A:K.209, A:K.213, A:K.213 G4P.6: 18 residues within 4Å: Chain B: R.74, S.100, D.121, C.124, A.125, R.128, I.129, S.130, N.147, E.191, K.192, T.207, V.208, K.209, K.213 Ligands: ATP.5, MG.7, MG.8 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:S.100, B:S.100, B:R.128, B:R.128, B:S.130, B:N.147, B:N.147, B:E.191, B:K.209 Water bridges: B:R.128, B:R.128, B:K.192, B:V.208, B:K.209, B:K.213, B:K.213, B:K.213 Salt bridges: B:R.74, B:D.121, B:R.128, B:R.128, B:K.192, B:K.209, B:K.209, B:K.213, B:K.213 G4P.10: 16 residues within 4Å: Chain C: R.74, D.121, C.124, A.125, R.128, I.129, S.130, N.147, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.9, MG.11, MG.12 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:S.130, C:N.147, C:N.147, C:E.191, C:K.209 Water bridges: C:S.100, C:D.121, C:S.130, C:S.130, C:K.192, C:V.208 Salt bridges: C:R.74, C:D.121, C:R.128, C:R.128, C:K.192, C:K.209, C:K.209, C:K.213, C:K.213 G4P.14: 17 residues within 4Å: Chain D: R.74, S.100, D.121, C.124, A.125, R.128, I.129, S.130, N.147, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.13, MG.15, MG.16 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:S.130, D:S.130, D:N.147, D:N.147, D:E.191, D:K.209 Water bridges: D:S.130, D:S.130, D:K.192, D:V.208, D:K.209, D:K.213, D:K.213, D:K.213 Salt bridges: D:R.74, D:D.121, D:R.128, D:R.128, D:K.192, D:K.209, D:K.209, D:K.213, D:K.213 G4P.18: 17 residues within 4Å: Chain E: R.74, D.121, C.124, A.125, R.128, I.129, S.130, N.147, M.150, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.17, MG.19, MG.20 23 PLIP interactions: 23 interactions with chain E Hydrogen bonds: E:R.128, E:R.128, E:S.130, E:S.130, E:N.147, E:N.147, E:K.209 Water bridges: E:S.130, E:S.130, E:K.192, E:K.209, E:K.213, E:K.213, E:K.213 Salt bridges: E:R.74, E:D.121, E:R.128, E:R.128, E:K.192, E:K.209, E:K.209, E:K.213, E:K.213 G4P.22: 17 residues within 4Å: Chain F: R.74, S.100, D.121, C.124, A.125, R.128, I.129, S.130, N.147, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.21, MG.23, MG.24 21 PLIP interactions: 21 interactions with chain F Hydrogen bonds: F:R.128, F:R.128, F:S.130, F:S.130, F:N.147, F:N.147, F:K.209 Water bridges: F:S.130, F:S.130, F:K.192, F:V.208, F:K.209 Salt bridges: F:R.74, F:D.121, F:R.128, F:R.128, F:K.192, F:K.209, F:K.209, F:K.213, F:K.213 G4P.26: 17 residues within 4Å: Chain G: R.74, S.100, D.121, C.124, A.125, R.128, I.129, S.130, N.147, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.25, MG.27, MG.28 22 PLIP interactions: 22 interactions with chain G Hydrogen bonds: G:S.130, G:N.147, G:N.147, G:K.209 Water bridges: G:R.128, G:R.128, G:R.128, G:S.130, G:S.130, G:K.192, G:V.208, G:K.209, G:K.213 Salt bridges: G:R.74, G:D.121, G:R.128, G:R.128, G:K.192, G:K.209, G:K.209, G:K.213, G:K.213 G4P.30: 18 residues within 4Å: Chain H: R.74, S.100, D.121, C.124, A.125, R.128, I.129, S.130, N.147, M.150, E.191, K.192, V.208, K.209, K.213 Ligands: ATP.29, MG.31, MG.32 19 PLIP interactions: 19 interactions with chain H Hydrogen bonds: H:S.130, H:S.130, H:N.147, H:N.147 Water bridges: H:R.128, H:S.130, H:S.130, H:S.130, H:E.191, H:K.192, H:V.208 Salt bridges: H:R.74, H:D.121, H:R.128, H:R.128, H:K.209, H:K.209, H:K.213, H:K.213

16 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: S.130, E.191, K.192 Ligands: ATP.1, G4P.2, MG.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.191, H2O.2 MG.4: 6 residues within 4Å: Chain A: E.191 Chain G: R.148 Ligands: ATP.1, G4P.2, MG.3, ATP.25 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.191, H2O.1, H2O.58 MG.7: 6 residues within 4Å: Chain B: S.130, E.191, K.192 Ligands: ATP.5, G4P.6, MG.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.191, H2O.12 MG.8: 6 residues within 4Å: Chain B: E.191 Chain H: R.148 Ligands: ATP.5, G4P.6, MG.7, ATP.29 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.191, H2O.66, H2O.67 MG.11: 6 residues within 4Å: Chain C: S.130, E.191, K.192 Ligands: ATP.9, G4P.10, MG.12 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.191, H2O.20 MG.12: 6 residues within 4Å: Chain C: E.191 Chain D: R.148 Ligands: ATP.9, G4P.10, MG.11, ATP.13 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.191, H2O.22, H2O.36 MG.15: 6 residues within 4Å: Chain C: R.148 Chain D: E.191 Ligands: ATP.9, ATP.13, G4P.14, MG.16 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.191, H2O.22, H2O.34 MG.16: 6 residues within 4Å: Chain D: S.130, E.191, K.192 Ligands: ATP.13, G4P.14, MG.15 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.191, H2O.33 MG.19: 5 residues within 4Å: Chain E: E.191 Chain F: R.148 Ligands: ATP.17, G4P.18, ATP.21 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.191, H2O.43 MG.20: 4 residues within 4Å: Chain E: S.130, E.191 Ligands: ATP.17, G4P.18 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.191, H2O.43 MG.23: 5 residues within 4Å: Chain F: S.130, E.191 Ligands: ATP.21, G4P.22, MG.24 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.191, H2O.52 MG.24: 6 residues within 4Å: Chain E: R.148 Chain F: E.191 Ligands: ATP.17, ATP.21, G4P.22, MG.23 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.191, H2O.43, H2O.52 MG.27: 6 residues within 4Å: Chain G: S.130, E.191, K.192 Ligands: ATP.25, G4P.26, MG.28 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.191, H2O.58 MG.28: 6 residues within 4Å: Chain A: R.148 Chain G: E.191 Ligands: ATP.1, ATP.25, G4P.26, MG.27 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.191, H2O.4, H2O.58 MG.31: 5 residues within 4Å: Chain H: S.130, E.191 Ligands: ATP.29, G4P.30, MG.32 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.191, H2O.66 MG.32: 6 residues within 4Å: Chain B: R.148 Chain H: E.191 Ligands: ATP.5, ATP.29, G4P.30, MG.31 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.191, H2O.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez-Justel, D. et al., Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase. Protein Sci. (2022)

Release Date

2022-05-11

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
G

F
J

G
L

H
N

Inosine-5'-monophosphate dehydrogenase

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