- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-14-mer
- Ligands
- 12 x D4E: (6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-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)
- 12 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.2, H2O.2
MG.3: 3 residues within 4Å:- Chain A: N.173, F.174, L.175
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:F.174
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.3, H2O.4
MG.9: 3 residues within 4Å:- Chain C: I.81, I.84, P.86
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:I.81, C:P.86, H2O.6
MG.15: 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.9, H2O.9
MG.18: 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.9, H2O.10
MG.20: 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.11, H2O.12
MG.24: 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.14, H2O.15
MG.26: 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.16, H2O.16
MG.29: 4 residues within 4Å:- Chain K: I.81, I.84, P.86, V.88
3 PLIP interactions:2 interactions with chain K, 1 Ligand-Water interactions- Metal complexes: K:I.81, K:P.86, H2O.17
MG.34: 4 residues within 4Å:- Chain M: I.81, I.84, P.86, V.88
3 PLIP interactions:2 interactions with chain M, 1 Ligand-Water interactions- Metal complexes: M:I.81, M:P.86, H2O.18
MG.38: 3 residues within 4Å:- Chain N: I.81, I.84, P.86
3 PLIP interactions:2 interactions with chain N, 1 Ligand-Water interactions- Metal complexes: N:I.81, N:P.86, H2O.19
- 15 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.4: 9 residues within 4Å:- Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.71, A:F.102, A:L.150
- Hydrogen bonds: A:H.123, A:H.123
MPD.6: 9 residues within 4Å:- Chain B: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:F.102, B:I.122, B:L.150, B:L.154, B:T.169
- Hydrogen bonds: B:H.123, B:H.123
MPD.7: 6 residues within 4Å:- Chain A: F.50, A.53, Q.54
- Chain B: E.9, R.23
- Ligands: D4E.1
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:F.50, A:A.53
- Hydrogen bonds: B:R.23
MPD.10: 9 residues within 4Å:- Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:V.71, C:F.102, C:L.150, C:L.154
- Hydrogen bonds: C:H.123, C:H.123
MPD.11: 8 residues within 4Å:- Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:V.71, D:F.102, D:L.150
- Hydrogen bonds: D:H.123, D:H.123
MPD.14: 9 residues within 4Å:- Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
7 PLIP interactions:7 interactions with chain E- Hydrophobic interactions: E:V.71, E:F.102, E:L.150, E:L.154
- Hydrogen bonds: E:H.123, E:H.123
- Water bridges: E:M.99
MPD.16: 9 residues within 4Å:- Chain F: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154
5 PLIP interactions:5 interactions with chain F- Hydrophobic interactions: F:F.102, F:L.150, F:L.154
- Hydrogen bonds: F:H.123, F:H.123
MPD.19: 11 residues within 4Å:- Chain G: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154, T.169
7 PLIP interactions:7 interactions with chain G- Hydrophobic interactions: G:F.102, G:L.150, G:L.154, G:T.169
- Hydrogen bonds: G:H.123
- Water bridges: G:S.98, G:M.99
MPD.21: 8 residues within 4Å:- Chain H: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150
5 PLIP interactions:5 interactions with chain H- Hydrophobic interactions: H:F.102, H:P.125, H:L.150
- Hydrogen bonds: H:S.98, H:H.123
MPD.25: 10 residues within 4Å:- Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169
8 PLIP interactions:8 interactions with chain I- Hydrophobic interactions: I:V.71, I:F.102, I:I.122, I:L.150, I:L.154, I:T.169
- Hydrogen bonds: I:H.123, I:H.123
MPD.27: 9 residues within 4Å:- Chain J: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
6 PLIP interactions:6 interactions with chain J- Hydrophobic interactions: J:V.71, J:F.102, J:L.150, J:L.154
- Hydrogen bonds: J:H.123, J:H.123
MPD.30: 7 residues within 4Å:- Chain K: S.98, M.99, S.101, I.122, H.123, Q.124, L.154
4 PLIP interactions:4 interactions with chain K- Hydrophobic interactions: K:I.122, K:L.154
- Hydrogen bonds: K:H.123, K:H.123
MPD.32: 9 residues within 4Å:- Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154
6 PLIP interactions:6 interactions with chain L- Hydrophobic interactions: L:V.71, L:F.102, L:L.150, L:L.154
- Hydrogen bonds: L:H.123, L:H.123
MPD.35: 8 residues within 4Å:- Chain M: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150
5 PLIP interactions:5 interactions with chain M- Hydrophobic interactions: M:F.102, M:P.125, M:L.150
- Hydrogen bonds: M:H.123, M:H.123
MPD.39: 9 residues within 4Å:- Chain N: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, T.169
7 PLIP interactions:7 interactions with chain N- Hydrophobic interactions: N:F.102, N:P.125, N:L.150, N:T.169
- Hydrogen bonds: N:S.98, N:H.123
- Water bridges: N:M.99
- 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 2.15 Å
- Oligo State
- homo-14-mer
- Ligands
- 12 x D4E: (6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-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)
- 12 x MG: MAGNESIUM ION(Non-covalent)
- 15 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