SMTL ID : 7mhb.1

Crystal structure of ATP-dependent protease ATPase subunit HslU in complex with Adenosine 5'-diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-12-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 Ligands: EDO.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:I.17, A:I.17, A:G.59, A:V.60, A:G.61, A:K.62, A:T.63, A:T.63, A:T.63, A:E.64, A:E.64 Water bridges: A:K.79, A:R.383 Salt bridges: A:K.62, A:R.383, A:R.383 ADP.7: 14 residues within 4Å: Chain B: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:I.17, B:I.17, B:T.58, B:G.59, B:V.60, B:G.61, B:K.62, B:T.63, B:E.64, B:E.64 Salt bridges: B:K.62, B:R.383, B:R.383 ADP.13: 15 residues within 4Å: Chain C: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 Ligands: EDO.18 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:I.17, C:I.17, C:G.59, C:V.60, C:G.61, C:K.62, C:T.63, C:T.63, C:T.63, C:E.64, C:E.64 Water bridges: C:K.79, C:R.383 Salt bridges: C:K.62, C:R.383, C:R.383 ADP.19: 14 residues within 4Å: Chain D: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:I.17, D:I.17, D:T.58, D:G.59, D:V.60, D:G.61, D:K.62, D:T.63, D:E.64, D:E.64 Salt bridges: D:K.62, D:R.383, D:R.383 ADP.25: 15 residues within 4Å: Chain E: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 Ligands: EDO.30 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:I.17, E:I.17, E:G.59, E:V.60, E:G.61, E:K.62, E:T.63, E:T.63, E:T.63, E:E.64, E:E.64 Water bridges: E:K.79, E:R.383 Salt bridges: E:K.62, E:R.383, E:R.383 ADP.31: 14 residues within 4Å: Chain F: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:I.17, F:I.17, F:T.58, F:G.59, F:V.60, F:G.61, F:K.62, F:T.63, F:E.64, F:E.64 Salt bridges: F:K.62, F:R.383, F:R.383 ADP.37: 15 residues within 4Å: Chain G: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 Ligands: EDO.42 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:I.17, G:I.17, G:T.58, G:G.59, G:V.60, G:G.61, G:K.62, G:T.63, G:T.63, G:E.64, G:E.64 Water bridges: G:E.64, G:K.79, G:R.383 Salt bridges: G:K.62, G:R.383, G:R.383 ADP.43: 14 residues within 4Å: Chain H: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:I.17, H:I.17, H:G.59, H:V.60, H:G.61, H:K.62, H:T.63, H:T.63, H:E.64, H:E.64 Salt bridges: H:K.62, H:R.383, H:R.383 ADP.49: 15 residues within 4Å: Chain I: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 Ligands: EDO.54 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:I.17, I:I.17, I:T.58, I:G.59, I:V.60, I:G.61, I:K.62, I:T.63, I:T.63, I:E.64, I:E.64 Water bridges: I:E.64, I:K.79, I:R.383 Salt bridges: I:K.62, I:R.383, I:R.383 ADP.55: 14 residues within 4Å: Chain J: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:I.17, J:I.17, J:G.59, J:V.60, J:G.61, J:K.62, J:T.63, J:T.63, J:E.64, J:E.64 Salt bridges: J:K.62, J:R.383, J:R.383 ADP.61: 15 residues within 4Å: Chain K: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 Ligands: EDO.66 17 PLIP interactions: 17 interactions with chain K Hydrogen bonds: K:I.17, K:I.17, K:T.58, K:G.59, K:V.60, K:G.61, K:K.62, K:T.63, K:T.63, K:E.64, K:E.64 Water bridges: K:E.64, K:K.79, K:R.383 Salt bridges: K:K.62, K:R.383, K:R.383 ADP.67: 14 residues within 4Å: Chain L: F.15, I.16, I.17, T.58, G.59, V.60, G.61, K.62, T.63, E.64, L.325, I.333, A.382, R.383 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:I.17, L:I.17, L:G.59, L:V.60, L:G.61, L:K.62, L:T.63, L:T.63, L:E.64, L:E.64 Salt bridges: L:K.62, L:R.383, L:R.383

36 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: D.13, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: S.359, D.361, D.411, A.412 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: I.16, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: S.359, D.361, A.362, D.411, A.412 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain C: D.13, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain C: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: S.359, D.361, D.411, A.412 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain D: I.16, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain D: S.359, D.361, A.362, D.411, A.412 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain E: D.13, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain E: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain E: S.359, D.361, D.411, A.412 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain F: I.16, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain F: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain F: S.359, D.361, A.362, D.411, A.412 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain G: D.13, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain G: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain G: S.359, D.361, D.411, A.412 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain H: I.16, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain H: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain H: S.359, D.361, A.362, D.411, A.412 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain I: D.13, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain I: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain I: S.359, D.361, D.411, A.412 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain J: I.16, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain J: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain J: S.359, D.361, A.362, D.411, A.412 Ligand excluded by PLIP SO4.62: 5 residues within 4Å: Chain K: D.13, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain K: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain K: S.359, D.361, D.411, A.412 Ligand excluded by PLIP SO4.68: 5 residues within 4Å: Chain L: I.16, I.17, G.18, K.23, R.332 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain L: P.57, T.58, A.299, H.301 Ligand excluded by PLIP SO4.70: 5 residues within 4Å: Chain L: S.359, D.361, A.362, D.411, A.412 Ligand excluded by PLIP

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 1 residues within 4Å: Chain A: N.379 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: E.64, A.339, L.341, Q.344 Ligands: ADP.1 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain B: N.379 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: L.325, F.330, V.371, N.374, N.379 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain C: N.379 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: E.64, A.339, L.341, Q.344 Ligands: ADP.13 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain D: N.379 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain D: L.325, F.330, V.371, N.374, N.379 Ligand excluded by PLIP EDO.29: 1 residues within 4Å: Chain E: N.379 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain E: E.64, A.339, L.341, Q.344 Ligands: ADP.25 Ligand excluded by PLIP EDO.35: 1 residues within 4Å: Chain F: N.379 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain F: L.325, F.330, V.371, N.374, N.379 Ligand excluded by PLIP EDO.41: 1 residues within 4Å: Chain G: N.379 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain G: E.64, A.339, L.341, Q.344 Ligands: ADP.37 Ligand excluded by PLIP EDO.47: 1 residues within 4Å: Chain H: N.379 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain H: L.325, F.330, V.371, N.374, N.379 Ligand excluded by PLIP EDO.53: 1 residues within 4Å: Chain I: N.379 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain I: E.64, A.339, L.341, Q.344 Ligands: ADP.49 Ligand excluded by PLIP EDO.59: 1 residues within 4Å: Chain J: N.379 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain J: L.325, F.330, V.371, N.374, N.379 Ligand excluded by PLIP EDO.65: 1 residues within 4Å: Chain K: N.379 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain K: E.64, A.339, L.341, Q.344 Ligands: ADP.61 Ligand excluded by PLIP EDO.71: 1 residues within 4Å: Chain L: N.379 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain L: L.325, F.330, V.371, N.374, N.379 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of ATP-dependent protease ATPase subunit HslU in complex with Adenosine 5'-diphosphate. to be published

Release Date

2021-04-28

Peptides

ATP-dependent protease ATPase subunit HslU: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

ATP-dependent protease ATPase subunit HslU