SMTL ID : 8qqr.1

Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP+ppGpp-bound form, super-compressed

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: S.139, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Chain E: R.157, K.198, E.200 Ligands: G4P.2, MG.3, MG.4, ATP.17, MG.19 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:S.139, A:T.155, A:N.156, A:N.156, A:R.157, A:D.158, A:I.179, A:I.179, A:E.200, A:E.200, E:R.157, E:E.200 Salt bridges: A:R.157, A:R.157, A:K.201, A:K.201, E:R.157, E:R.157 ATP.5: 21 residues within 4Å: Chain B: S.139, I.153, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Chain F: R.157, K.198, E.200 Ligands: G4P.6, MG.7, MG.8, ATP.21, MG.23 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:S.139, B:T.155, B:N.156, B:N.156, B:R.157, B:D.158, B:I.179, B:I.179, B:E.200, B:E.200 Salt bridges: B:R.157, B:R.157, B:K.201, B:K.201, F:R.157, F:R.157, F:R.157 ATP.9: 20 residues within 4Å: Chain C: S.139, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Chain G: R.157, K.198, E.200 Ligands: G4P.10, MG.11, MG.12, ATP.25, MG.27 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain G Hydrogen bonds: C:S.139, C:T.155, C:N.156, C:N.156, C:R.157, C:D.158, C:I.179, C:I.179, C:E.200, C:E.200, C:E.200 Salt bridges: C:R.157, C:R.157, C:K.201, C:K.201, G:R.157, G:R.157, G:R.157 ATP.13: 21 residues within 4Å: Chain D: S.139, I.153, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Chain H: R.157, K.198, E.200 Ligands: G4P.14, MG.15, MG.16, ATP.29, MG.31 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain H Hydrogen bonds: D:S.139, D:T.155, D:N.156, D:N.156, D:R.157, D:D.158, D:I.179, D:I.179, D:E.200, D:E.200, H:R.157 Salt bridges: D:R.157, D:R.157, D:K.201, D:K.201, H:R.157, H:R.157 ATP.17: 21 residues within 4Å: Chain A: R.157, K.198, E.200 Chain E: S.139, I.153, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Ligands: ATP.1, MG.3, G4P.18, MG.19, MG.20 19 PLIP interactions: 4 interactions with chain A, 15 interactions with chain E Hydrogen bonds: A:E.200, E:S.139, E:T.155, E:N.156, E:N.156, E:R.157, E:D.158, E:T.174, E:I.179, E:I.179, E:E.200, E:E.200 Salt bridges: A:R.157, A:R.157, A:R.157, E:R.157, E:R.157, E:K.201, E:K.201 ATP.21: 21 residues within 4Å: Chain B: R.157, K.198, E.200 Chain F: S.139, I.153, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Ligands: ATP.5, MG.7, G4P.22, MG.23, MG.24 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:S.139, F:T.155, F:N.156, F:N.156, F:R.157, F:D.158, F:T.174, F:I.179, F:I.179, F:E.200, F:E.200, B:R.157 Salt bridges: F:R.157, F:R.157, F:K.201, F:K.201, B:R.157, B:R.157 ATP.25: 22 residues within 4Å: Chain C: R.157, K.198, E.200 Chain G: S.139, I.153, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Ligands: ATP.9, G4P.10, MG.11, G4P.26, MG.27, MG.28 18 PLIP interactions: 15 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:S.139, G:T.155, G:N.156, G:N.156, G:R.157, G:D.158, G:T.174, G:I.179, G:I.179, G:E.200, G:E.200 Salt bridges: G:R.157, G:R.157, G:K.201, G:K.201, C:R.157, C:R.157, C:R.157 ATP.29: 22 residues within 4Å: Chain D: R.157, K.198, E.200 Chain H: S.139, I.153, T.155, N.156, R.157, D.158, T.174, L.178, I.179, I.199, E.200, K.201, P.203 Ligands: ATP.13, G4P.14, MG.15, G4P.30, MG.31, MG.32 19 PLIP interactions: 15 interactions with chain H, 4 interactions with chain D Hydrogen bonds: H:S.139, H:T.155, H:N.156, H:N.156, H:R.157, H:D.158, H:T.174, H:I.179, H:I.179, H:E.200, H:E.200, D:E.200 Salt bridges: H:R.157, H:R.157, H:K.201, H:K.201, D:R.157, D:R.157, D:R.157

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

G4P.2: 14 residues within 4Å: Chain A: R.83, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Chain E: R.160 Ligands: ATP.1, MG.3, MG.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:I.138, A:S.139, A:N.156 Salt bridges: A:R.83, A:D.130, A:R.137, A:R.137, A:K.201, A:K.218, A:K.218, A:K.222, A:K.222, E:R.160 G4P.6: 15 residues within 4Å: Chain B: R.83, D.130, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Chain F: R.160 Ligands: ATP.5, MG.7, MG.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:S.139, B:N.156 Salt bridges: B:R.83, B:D.130, B:R.137, B:R.137, B:K.201, B:K.218, B:K.218, B:K.222, B:K.222, F:R.160 G4P.10: 15 residues within 4Å: Chain C: R.83, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Chain G: R.160 Ligands: ATP.9, MG.11, MG.12, ATP.25 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:S.139, C:N.156 Salt bridges: C:R.83, C:D.130, C:R.137, C:R.137, C:K.201, C:K.218, C:K.218, C:K.222, C:K.222, G:R.160 G4P.14: 16 residues within 4Å: Chain D: R.83, D.130, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Chain H: R.160 Ligands: ATP.13, MG.15, MG.16, ATP.29 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:S.139, D:S.139, D:N.156 Salt bridges: D:R.83, D:D.130, D:R.137, D:K.201, D:K.218, D:K.218, D:K.222, D:K.222, H:R.160 G4P.18: 14 residues within 4Å: Chain A: R.160 Chain E: R.83, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Ligands: ATP.17, MG.19, MG.20 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.139, E:N.156 Salt bridges: E:R.83, E:D.130, E:R.137, E:R.137, E:K.201, E:K.218, E:K.218, E:K.222, E:K.222, A:R.160 G4P.22: 14 residues within 4Å: Chain B: R.160 Chain F: R.83, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Ligands: ATP.21, MG.23, MG.24 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:S.139, F:N.156 Salt bridges: F:R.83, F:D.130, F:R.137, F:R.137, F:K.201, F:K.218, F:K.218, F:K.222, F:K.222, B:R.160 G4P.26: 14 residues within 4Å: Chain C: R.160 Chain G: R.83, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Ligands: ATP.25, MG.27, MG.28 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:S.139, G:N.156 Salt bridges: G:R.83, G:D.130, G:R.137, G:K.201, G:K.218, G:K.218, G:K.222, G:K.222, C:R.160 G4P.30: 14 residues within 4Å: Chain D: R.160 Chain H: R.83, C.133, A.134, R.137, I.138, S.139, N.156, E.200, K.218, K.222 Ligands: ATP.29, MG.31, MG.32 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain H Salt bridges: D:R.160, H:R.83, H:D.130, H:R.137, H:R.137, H:K.218, H:K.218, H:K.222, H:K.222 Hydrogen bonds: H:I.138, H:S.139, H:S.139, H:N.156

16 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: E.200 Chain E: R.157 Ligands: ATP.1, G4P.2, MG.4, ATP.17 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.200 MG.4: 5 residues within 4Å: Chain A: S.139, E.200 Ligands: ATP.1, G4P.2, MG.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.200 MG.7: 6 residues within 4Å: Chain B: E.200 Chain F: R.157 Ligands: ATP.5, G4P.6, MG.8, ATP.21 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.200 MG.8: 5 residues within 4Å: Chain B: S.139, E.200 Ligands: ATP.5, G4P.6, MG.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.200 MG.11: 6 residues within 4Å: Chain C: E.200 Chain G: R.160 Ligands: ATP.9, G4P.10, MG.12, ATP.25 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.200 MG.12: 5 residues within 4Å: Chain C: S.139, E.200 Ligands: ATP.9, G4P.10, MG.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.200 MG.15: 6 residues within 4Å: Chain D: E.200 Chain H: R.157 Ligands: ATP.13, G4P.14, MG.16, ATP.29 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.200 MG.16: 5 residues within 4Å: Chain D: S.139, E.200 Ligands: ATP.13, G4P.14, MG.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.200 MG.19: 6 residues within 4Å: Chain A: R.160 Chain E: E.200 Ligands: ATP.1, ATP.17, G4P.18, MG.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.200 MG.20: 5 residues within 4Å: Chain E: S.139, E.200 Ligands: ATP.17, G4P.18, MG.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.200 MG.23: 6 residues within 4Å: Chain B: R.157 Chain F: E.200 Ligands: ATP.5, ATP.21, G4P.22, MG.24 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.200 MG.24: 5 residues within 4Å: Chain F: S.139, E.200 Ligands: ATP.21, G4P.22, MG.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.200 MG.27: 5 residues within 4Å: Chain G: E.200 Ligands: ATP.9, ATP.25, G4P.26, MG.28 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.200 MG.28: 5 residues within 4Å: Chain G: S.139, E.200 Ligands: ATP.25, G4P.26, MG.27 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.200 MG.31: 6 residues within 4Å: Chain D: R.157 Chain H: E.200 Ligands: ATP.13, ATP.29, G4P.30, MG.32 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.200, H:E.200 MG.32: 5 residues within 4Å: Chain H: S.139, E.200 Ligands: ATP.29, G4P.30, MG.31 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bulvas, O. et al., Deciphering the allosteric regulation of mycobacterial inosine-5'-monophosphate dehydrogenase. Nat Commun (2024)

Release Date

2024-08-14

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Inosine-5'-monophosphate dehydrogenase

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