SMTL ID : 7qdx.1

bacterial IMPDH chimera

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-octamer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.200 Ligands: MG.2, ATP.3, ATP.4 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: E.200 Ligands: MG.1, ATP.3, ATP.4, ATP.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.200, H2O.2 MG.5: 4 residues within 4Å: Chain B: E.200 Ligands: MG.6, ATP.7, ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.200 MG.6: 5 residues within 4Å: Chain B: E.200 Ligands: ATP.4, MG.5, ATP.7, ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.200 MG.9: 4 residues within 4Å: Chain C: E.200 Ligands: MG.10, ATP.11, ATP.12 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain C: E.200 Ligands: MG.9, ATP.11, ATP.12, ATP.15 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.200, H2O.3 MG.13: 4 residues within 4Å: Chain D: E.200 Ligands: MG.14, ATP.15, ATP.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.200 MG.14: 5 residues within 4Å: Chain D: E.200 Ligands: ATP.12, MG.13, ATP.15, ATP.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.200 MG.17: 4 residues within 4Å: Chain E: E.200 Ligands: MG.18, ATP.19, ATP.20 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain E: E.200 Ligands: MG.17, ATP.19, ATP.20, ATP.23 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.200, H2O.5 MG.21: 4 residues within 4Å: Chain F: E.200 Ligands: MG.22, ATP.23, ATP.24 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.200 MG.22: 5 residues within 4Å: Chain F: E.200 Ligands: ATP.20, MG.21, ATP.23, ATP.24 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.200 MG.25: 4 residues within 4Å: Chain G: E.200 Ligands: MG.26, ATP.27, ATP.28 No protein-ligand interaction detected (PLIP) MG.26: 5 residues within 4Å: Chain G: E.200 Ligands: MG.25, ATP.27, ATP.28, ATP.31 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.200, H2O.7 MG.29: 4 residues within 4Å: Chain H: E.200 Ligands: MG.30, ATP.31, ATP.32 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.200 MG.30: 5 residues within 4Å: Chain H: E.200 Ligands: ATP.28, MG.29, ATP.31, ATP.32 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.200

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

ATP.3: 16 residues within 4Å: Chain A: V.114, P.117, V.118, F.138, S.139, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.1, MG.2, ATP.4, ATP.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.118, A:S.139, A:G.140, A:E.200, A:T.216, A:D.219 Water bridges: A:R.218 Salt bridges: A:K.201, A:K.201, A:R.218, A:R.218, A:R.218 pi-Stacking: A:F.138, A:F.138 ATP.4: 20 residues within 4Å: Chain A: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Chain B: R.156, R.198, E.200 Ligands: MG.1, MG.2, ATP.3, MG.6, ATP.7 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.155, A:R.156, A:D.157, A:T.173, A:T.173, A:V.179, A:V.179, A:K.201, B:R.198 Salt bridges: A:R.156, A:R.156, A:K.201, A:K.201, B:R.156, B:R.156, B:R.156 ATP.7: 21 residues within 4Å: Chain A: R.156, R.198, E.200 Chain B: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Ligands: MG.2, ATP.3, ATP.4, MG.5, MG.6, ATP.8 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.154, B:G.155, B:R.156, B:D.157, B:T.173, B:V.179, B:V.179, B:E.200, B:E.200 Salt bridges: B:R.156, B:K.201, B:K.201, A:R.156, A:R.156, A:R.156 ATP.8: 15 residues within 4Å: Chain B: P.117, V.118, F.138, G.140, F.141, P.142, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.5, MG.6, ATP.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.118, B:G.140, B:D.219 Salt bridges: B:K.201, B:K.201, B:R.218, B:R.218, B:R.218 pi-Stacking: B:F.138, B:F.138 ATP.11: 16 residues within 4Å: Chain C: V.114, P.117, V.118, F.138, S.139, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.9, MG.10, ATP.12, ATP.15 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.118, C:S.139, C:G.140, C:E.200, C:T.216, C:D.219 Water bridges: C:R.218 Salt bridges: C:K.201, C:K.201, C:R.218, C:R.218, C:R.218 pi-Stacking: C:F.138, C:F.138 ATP.12: 20 residues within 4Å: Chain C: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Chain D: R.156, R.198, E.200 Ligands: MG.9, MG.10, ATP.11, MG.14, ATP.15 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.155, C:R.156, C:D.157, C:T.173, C:T.173, C:V.179, C:V.179, C:K.201, D:R.198 Salt bridges: C:R.156, C:R.156, C:K.201, C:K.201, D:R.156, D:R.156, D:R.156 ATP.15: 21 residues within 4Å: Chain C: R.156, R.198, E.200 Chain D: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Ligands: MG.10, ATP.11, ATP.12, MG.13, MG.14, ATP.16 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.154, D:G.155, D:R.156, D:D.157, D:T.173, D:V.179, D:V.179, D:E.200, D:E.200 Salt bridges: D:R.156, D:K.201, D:K.201, C:R.156, C:R.156, C:R.156 ATP.16: 15 residues within 4Å: Chain D: P.117, V.118, F.138, G.140, F.141, P.142, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.13, MG.14, ATP.15 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:V.118, D:G.140, D:E.200, D:D.219 Salt bridges: D:K.201, D:K.201, D:R.218, D:R.218, D:R.218 pi-Stacking: D:F.138, D:F.138 ATP.19: 16 residues within 4Å: Chain E: V.114, P.117, V.118, F.138, S.139, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.17, MG.18, ATP.20, ATP.23 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:V.118, E:S.139, E:G.140, E:E.200, E:T.216, E:D.219 Water bridges: E:R.218 Salt bridges: E:K.201, E:K.201, E:R.218, E:R.218, E:R.218 pi-Stacking: E:F.138, E:F.138 ATP.20: 20 residues within 4Å: Chain E: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Chain F: R.156, R.198, E.200 Ligands: MG.17, MG.18, ATP.19, MG.22, ATP.23 16 PLIP interactions: 12 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.155, E:R.156, E:D.157, E:T.173, E:T.173, E:V.179, E:V.179, E:K.201, F:R.198 Salt bridges: E:R.156, E:R.156, E:K.201, E:K.201, F:R.156, F:R.156, F:R.156 ATP.23: 21 residues within 4Å: Chain E: R.156, R.198, E.200 Chain F: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Ligands: MG.18, ATP.19, ATP.20, MG.21, MG.22, ATP.24 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:T.154, F:G.155, F:R.156, F:D.157, F:T.173, F:V.179, F:V.179, F:E.200, F:E.200 Salt bridges: F:R.156, F:K.201, F:K.201, E:R.156, E:R.156, E:R.156 ATP.24: 15 residues within 4Å: Chain F: P.117, V.118, F.138, G.140, F.141, P.142, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.21, MG.22, ATP.23 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:V.118, F:G.140, F:D.219 Salt bridges: F:K.201, F:K.201, F:R.218, F:R.218, F:R.218 pi-Stacking: F:F.138, F:F.138 ATP.27: 16 residues within 4Å: Chain G: V.114, P.117, V.118, F.138, S.139, G.140, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.25, MG.26, ATP.28, ATP.31 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:V.118, G:S.139, G:G.140, G:E.200, G:T.216, G:D.219 Water bridges: G:R.218 Salt bridges: G:K.201, G:K.201, G:R.218, G:R.218, G:R.218 pi-Stacking: G:F.138, G:F.138 ATP.28: 20 residues within 4Å: Chain G: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Chain H: R.156, R.198, E.200 Ligands: MG.25, MG.26, ATP.27, MG.30, ATP.31 16 PLIP interactions: 12 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:G.155, G:R.156, G:D.157, G:T.173, G:T.173, G:V.179, G:V.179, G:K.201, H:R.198 Salt bridges: G:R.156, G:R.156, G:K.201, G:K.201, H:R.156, H:R.156, H:R.156 ATP.31: 21 residues within 4Å: Chain G: R.156, R.198, E.200 Chain H: I.152, T.154, G.155, R.156, D.157, T.173, K.177, L.178, V.179, I.199, E.200, K.201 Ligands: MG.26, ATP.27, ATP.28, MG.29, MG.30, ATP.32 15 PLIP interactions: 12 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:T.154, H:G.155, H:R.156, H:D.157, H:T.173, H:V.179, H:V.179, H:E.200, H:E.200 Salt bridges: H:R.156, H:K.201, H:K.201, G:R.156, G:R.156, G:R.156 ATP.32: 15 residues within 4Å: Chain H: P.117, V.118, F.138, G.140, F.141, P.142, E.200, K.201, L.214, T.216, R.218, D.219 Ligands: MG.29, MG.30, ATP.31 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:V.118, H:G.140, H:E.200, H:D.219 Salt bridges: H:K.201, H:K.201, H:R.218, H:R.218, H:R.218 pi-Stacking: H:F.138, H:F.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gedeon, A. et al., Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases. Protein Sci. (2023)

Release Date

2023-06-14

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Inosine-5'-monophosphate dehydrogenase

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