SMTL ID : 5kwa.1

complete structure of the Mycobacterium tuberculosis proteasomal ATPase Mpa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: D.148, I.149, G.150, L.152, P.190, G.191, C.192, G.193, K.194, T.195, L.196, N.311, I.343, Y.347, G.411, A.412, Q.415 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.150, A:G.191, A:C.192, A:C.192, A:G.193, A:G.193, A:K.194, A:T.195, A:L.196, A:N.311 Water bridges: A:T.195 Salt bridges: A:K.194 ADP.3: 19 residues within 4Å: Chain B: D.148, I.149, G.150, L.152, P.190, G.191, C.192, G.193, K.194, T.195, L.196, N.311, I.343, Y.347, G.411, A.412, Q.415 Chain C: R.322 Ligands: MG.4 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.150, B:G.191, B:C.192, B:C.192, B:G.193, B:G.193, B:K.194, B:T.195, B:L.196, B:N.311, B:Y.347, B:G.411 Salt bridges: B:K.194, C:R.322 Water bridges: C:R.322, C:R.322 ADP.5: 18 residues within 4Å: Chain C: D.148, I.149, G.150, L.152, P.190, G.191, C.192, G.193, K.194, T.195, L.196, N.311, I.343, Y.347, G.411, A.412, Q.415 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.150, C:G.191, C:C.192, C:C.192, C:G.193, C:G.193, C:K.194, C:T.195, C:L.196, C:N.311 Water bridges: C:T.195 Salt bridges: C:K.194 ADP.7: 19 residues within 4Å: Chain D: D.148, I.149, G.150, L.152, P.190, G.191, C.192, G.193, K.194, T.195, L.196, N.311, I.343, Y.347, G.411, A.412, Q.415 Chain E: R.322 Ligands: MG.8 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.150, D:G.191, D:C.192, D:C.192, D:G.193, D:G.193, D:K.194, D:T.195, D:L.196, D:N.311, D:Y.347, D:G.411 Salt bridges: D:K.194, E:R.322 Water bridges: E:R.322, E:R.322 ADP.9: 18 residues within 4Å: Chain E: D.148, I.149, G.150, L.152, P.190, G.191, C.192, G.193, K.194, T.195, L.196, N.311, I.343, Y.347, G.411, A.412, Q.415 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.150, E:G.191, E:C.192, E:C.192, E:G.193, E:G.193, E:K.194, E:T.195, E:L.196, E:N.311 Water bridges: E:T.195 Salt bridges: E:K.194 ADP.11: 19 residues within 4Å: Chain A: R.322 Chain F: D.148, I.149, G.150, L.152, P.190, G.191, C.192, G.193, K.194, T.195, L.196, N.311, I.343, Y.347, G.411, A.412, Q.415 Ligands: MG.12 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.150, F:G.191, F:C.192, F:C.192, F:G.193, F:G.193, F:K.194, F:T.195, F:L.196, F:N.311, F:Y.347, F:G.411 Salt bridges: F:K.194, A:R.322 Water bridges: A:R.322, A:R.322

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.195 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.195, H2O.1 MG.4: 4 residues within 4Å: Chain B: T.195, D.266 Chain C: R.322 Ligands: ADP.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.195, H2O.1 MG.6: 2 residues within 4Å: Chain C: T.195 Ligands: ADP.5 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.195, H2O.2 MG.8: 4 residues within 4Å: Chain D: T.195, D.266 Chain E: R.322 Ligands: ADP.7 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.195, H2O.2 MG.10: 2 residues within 4Å: Chain E: T.195 Ligands: ADP.9 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.195, H2O.2 MG.12: 4 residues within 4Å: Chain A: R.322 Chain F: T.195, D.266 Ligands: ADP.11 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:T.195, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Y. et al., Mycobacterium tuberculosis proteasomal ATPase Mpa has a beta-grasp domain that hinders docking with the proteasome core protease. Mol. Microbiol. (2017)

Release Date

2017-06-07

Peptides

Proteasome-associated ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Proteasome-associated ATPase