- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-14-mer
- Ligands
- 14 x 9DF: (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide(Non-covalent)
- 13 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 3 residues within 4Å:- Chain A: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:I.81, A:P.86, H2O.4, H2O.4
MG.5: 3 residues within 4Å:- Chain B: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:I.81, B:P.86, H2O.7, H2O.9
MG.9: 3 residues within 4Å:- Chain C: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:I.81, C:P.86, H2O.13, H2O.13
MG.14: 3 residues within 4Å:- Chain E: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: E:I.81, E:P.86, H2O.21, H2O.21
MG.17: 3 residues within 4Å:- Chain F: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain F, 2 Ligand-Water interactions- Metal complexes: F:I.81, F:P.86, H2O.25, H2O.26
MG.20: 3 residues within 4Å:- Chain G: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain G, 2 Ligand-Water interactions- Metal complexes: G:I.81, G:P.86, H2O.29, H2O.30
MG.23: 3 residues within 4Å:- Chain H: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain H, 2 Ligand-Water interactions- Metal complexes: H:I.81, H:P.86, H2O.34, H2O.34
MG.26: 3 residues within 4Å:- Chain I: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain I, 2 Ligand-Water interactions- Metal complexes: I:I.81, I:P.86, H2O.39, H2O.39
MG.30: 3 residues within 4Å:- Chain J: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain J, 2 Ligand-Water interactions- Metal complexes: J:I.81, J:P.86, H2O.43, H2O.44
MG.33: 3 residues within 4Å:- Chain K: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain K, 2 Ligand-Water interactions- Metal complexes: K:I.81, K:P.86, H2O.47, H2O.49
MG.36: 3 residues within 4Å:- Chain L: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain L, 2 Ligand-Water interactions- Metal complexes: L:I.81, L:P.86, H2O.52, H2O.52
MG.39: 3 residues within 4Å:- Chain M: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain M, 2 Ligand-Water interactions- Metal complexes: M:I.81, M:P.86, H2O.54, H2O.56
MG.42: 3 residues within 4Å:- Chain N: I.81, I.84, P.86
4 PLIP interactions:2 interactions with chain N, 2 Ligand-Water interactions- Metal complexes: N:I.81, N:P.86, H2O.59, H2O.59
- 16 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.3: 9 residues within 4Å:- Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.6: 8 residues within 4Å:- Chain B: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.7: 6 residues within 4Å:- Chain A: F.50, A.53, Q.54
- Chain B: E.9, R.23
- Ligands: 9DF.4
Ligand excluded by PLIPMPD.10: 9 residues within 4Å:- Chain C: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169
Ligand excluded by PLIPMPD.12: 9 residues within 4Å:- Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.15: 8 residues within 4Å:- Chain E: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.18: 10 residues within 4Å:- Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169
Ligand excluded by PLIPMPD.21: 10 residues within 4Å:- Chain G: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, L.154, T.169
Ligand excluded by PLIPMPD.24: 9 residues within 4Å:- Chain H: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, L.154
Ligand excluded by PLIPMPD.27: 9 residues within 4Å:- Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.28: 6 residues within 4Å:- Chain H: F.50, A.53, Q.54
- Chain I: E.9, R.23
- Ligands: 9DF.25
Ligand excluded by PLIPMPD.31: 8 residues within 4Å:- Chain J: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.34: 7 residues within 4Å:- Chain K: S.98, M.99, S.101, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.37: 9 residues within 4Å:- Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
Ligand excluded by PLIPMPD.40: 9 residues within 4Å:- Chain M: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, L.154
Ligand excluded by PLIPMPD.43: 9 residues within 4Å:- Chain N: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, L.154
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wei, B. et al., Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP. Nat Commun (2022)
- Release Date
- 2022-11-16
- Peptides
- ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
N
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-14-mer
- Ligands
- 14 x 9DF: (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide(Non-covalent)
- 13 x MG: MAGNESIUM ION(Non-covalent)
- 16 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wei, B. et al., Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP. Nat Commun (2022)
- Release Date
- 2022-11-16
- Peptides
- ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
N