SMTL ID : 7nku.1

diazaborine bound Drg1(AFG2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)(Covalent)

AGS.1: 15 residues within 4Å: Chain A: A.246, G.248, G.289, T.290, G.291, K.292, T.293, M.294, E.346, N.390, I.422, Q.426, G.454, A.455, T.458 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.248, A:G.248, A:G.289, A:T.290, A:G.291, A:K.292, A:T.293, A:T.293, A:T.293, A:M.294, A:E.346 Salt bridges: A:K.292 AGS.2: 15 residues within 4Å: Chain A: I.518, G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, E.617, N.660, I.692, G.721 Ligands: TDB.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.519, A:G.519, A:G.560, A:K.563, A:T.564, A:T.564, A:T.564, A:L.565, A:E.617 Salt bridges: A:K.563, A:K.563 AGS.5: 17 residues within 4Å: Chain B: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, E.346, N.390, I.422, Q.426, G.454, A.455, T.458 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.248, B:G.248, B:G.289, B:G.291, B:K.292, B:K.292, B:T.293, B:T.293, B:T.293, B:M.294, B:E.346 Salt bridges: B:K.292 AGS.6: 16 residues within 4Å: Chain B: I.518, G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, D.616, E.617, I.692, G.721, A.722 Ligands: TDB.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.519, B:G.519, B:G.560, B:K.563, B:T.564, B:T.564, B:T.564, B:L.565, B:E.617 Salt bridges: B:K.563, B:K.563 AGS.8: 14 residues within 4Å: Chain C: A.246, V.247, G.248, G.289, T.290, G.291, K.292, T.293, M.294, E.346, I.422, G.454, A.455, T.458 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.248, C:G.248, C:G.289, C:G.291, C:K.292, C:T.293, C:T.293, C:T.293, C:M.294, C:E.346 AGS.9: 16 residues within 4Å: Chain C: G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, D.616, E.617, N.660, I.692, G.721, A.722 Ligands: TDB.10 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.519, C:G.560, C:K.563, C:T.564, C:T.564, C:T.564, C:L.565, C:E.617, C:N.660 Salt bridges: C:K.563 AGS.11: 14 residues within 4Å: Chain D: A.246, G.248, G.289, T.290, G.291, K.292, T.293, M.294, E.346, N.390, I.422, G.454, A.455, T.458 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.248, D:G.248, D:G.289, D:T.290, D:G.291, D:K.292, D:K.292, D:T.293, D:T.293, D:M.294, D:E.346 Salt bridges: D:K.292 AGS.12: 19 residues within 4Å: Chain D: D.517, I.518, G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, D.616, E.617, N.660, I.692, G.721, A.722 Chain E: R.674 Ligands: TDB.13 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.519, D:G.519, D:G.560, D:K.563, D:T.564, D:T.564, D:T.564, D:L.565, D:E.617, E:R.674 Salt bridges: D:K.563 AGS.14: 18 residues within 4Å: Chain E: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, E.346, N.390, I.422, Q.426, G.454, A.455, T.458 Chain F: R.404 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.248, E:G.248, E:G.289, E:T.290, E:G.291, E:K.292, E:T.293, E:T.293, E:T.293, E:M.294, F:R.404 Salt bridges: E:K.292 AGS.15: 16 residues within 4Å: Chain E: I.518, G.519, P.559, G.560, C.561, S.562, K.563, T.564, L.565, D.616, E.617, A.658, I.692, G.721, A.722 Ligands: TDB.16 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.519, E:G.560, E:S.562, E:K.563, E:T.564, E:T.564, E:T.564, E:D.616 Salt bridges: E:K.563 AGS.17: 17 residues within 4Å: Chain A: R.404 Chain F: A.246, V.247, G.248, P.288, G.289, T.290, G.291, K.292, T.293, M.294, E.346, I.422, Q.426, G.454, A.455, T.458 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.248, F:G.248, F:G.289, F:T.290, F:G.291, F:K.292, F:T.293, F:T.293, F:T.293, F:M.294, F:E.346, F:E.346, F:Q.426 Salt bridges: F:K.292 AGS.18: 17 residues within 4Å: Chain A: R.674 Chain F: D.517, I.518, G.519, P.558, P.559, G.560, C.561, S.562, K.563, T.564, L.565, N.660, I.692, G.721, A.722 Ligands: TDB.4 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.519, F:G.519, F:G.560, F:K.563, F:T.564, F:T.564, F:L.565, F:N.660 Salt bridges: F:K.563

6 x TDB: 6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL(Non-covalent)

TDB.3: 5 residues within 4Å: Chain A: L.565, V.725, Q.729 Chain B: G.673 Ligands: AGS.2 No protein-ligand interaction detected (PLIP) TDB.4: 5 residues within 4Å: Chain A: G.673 Chain F: L.565, K.695, V.725 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.695 TDB.7: 6 residues within 4Å: Chain B: L.565, K.695, V.725 Chain C: V.647, G.673 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.695 TDB.10: 4 residues within 4Å: Chain C: L.565, V.725 Chain D: G.673 Ligands: AGS.9 No protein-ligand interaction detected (PLIP) TDB.13: 5 residues within 4Å: Chain D: L.565, V.725, Q.729 Chain E: G.673 Ligands: AGS.12 No protein-ligand interaction detected (PLIP) TDB.16: 4 residues within 4Å: Chain E: L.565, V.725 Chain F: G.673 Ligands: AGS.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prattes, M. et al., Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nat Commun (2021)

Release Date

2021-06-23

Peptides

ATPase family gene 2 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATPase family gene 2 protein

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