- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.28 Å
- Oligo State
- hetero-14-14-mer
- Ligands
- 14 x U5Y: (12S,15S)-N-[(2-fluorophenyl)methyl]-10,13-dioxo-12-{2-oxo-2-[(2R)-2-phenylpyrrolidin-1-yl]ethyl}-2-oxa-11,14-diazatricyclo[15.2.2.1~3,7~]docosa-1(19),3(22),4,6,17,20-hexaene-15-carboxamide(Non-covalent)
U5Y.1: 21 residues within 4Å:- Chain H: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, G.97
- Chain I: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.2
19 PLIP interactions:15 interactions with chain H, 4 interactions with chain I- Hydrophobic interactions: H:V.31, H:V.31, H:K.33, H:K.33, H:A.49, H:A.52, I:D.124, I:N.130
- Hydrogen bonds: H:T.1, H:T.21, H:T.21, H:Q.22, H:S.27, H:G.47, H:A.49, I:D.124, I:D.124
- Water bridges: H:G.23, H:A.50
U5Y.3: 20 residues within 4Å:- Chain I: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain J: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.4
17 PLIP interactions:13 interactions with chain I, 4 interactions with chain J- Hydrophobic interactions: I:V.31, I:V.31, I:K.33, I:K.33, I:A.49, I:A.52, J:D.124, J:N.130
- Hydrogen bonds: I:T.21, I:T.21, I:Q.22, I:S.27, I:G.47, I:A.49, J:D.124, J:D.124
- Water bridges: I:A.50
U5Y.5: 21 residues within 4Å:- Chain J: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, G.97
- Chain K: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.6
17 PLIP interactions:13 interactions with chain J, 4 interactions with chain K- Hydrophobic interactions: J:V.31, J:V.31, J:K.33, J:K.33, J:A.49, J:A.52, K:D.124, K:N.130
- Hydrogen bonds: J:T.21, J:T.21, J:Q.22, J:S.27, J:G.47, J:A.49, K:D.124, K:D.124
- Water bridges: J:A.50
U5Y.7: 21 residues within 4Å:- Chain K: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain L: S.122, F.123, D.124, A.126, G.128, W.129, N.130
- Ligands: CIT.8
19 PLIP interactions:5 interactions with chain L, 14 interactions with chain K- Hydrophobic interactions: L:D.124, L:A.126, L:N.130, K:V.31, K:V.31, K:K.33, K:K.33, K:A.49, K:A.52
- Hydrogen bonds: L:D.124, L:D.124, K:T.1, K:T.21, K:T.21, K:Q.22, K:S.27, K:G.47, K:A.49
- Water bridges: K:A.50
U5Y.9: 20 residues within 4Å:- Chain L: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain M: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.10
17 PLIP interactions:14 interactions with chain L, 3 interactions with chain M- Hydrophobic interactions: L:V.31, L:V.31, L:K.33, L:K.33, L:A.49, L:A.52, M:D.124, M:N.130
- Hydrogen bonds: L:T.1, L:T.21, L:T.21, L:Q.22, L:S.27, L:G.47, L:A.49, M:D.124
- Water bridges: L:A.50
U5Y.11: 21 residues within 4Å:- Chain M: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain N: S.122, F.123, D.124, A.126, G.128, W.129, N.130
- Ligands: CIT.12
15 PLIP interactions:4 interactions with chain N, 11 interactions with chain M- Hydrophobic interactions: N:D.124, N:A.126, N:N.130, M:V.31, M:K.33, M:A.49, M:A.52
- Hydrogen bonds: N:D.124, M:T.1, M:T.21, M:T.21, M:Q.22, M:S.27, M:G.47, M:A.49
U5Y.13: 22 residues within 4Å:- Chain H: S.122, F.123, D.124, A.126, G.128, W.129, N.130
- Chain N: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, G.97
- Ligands: CIT.14
19 PLIP interactions:15 interactions with chain N, 4 interactions with chain H- Hydrophobic interactions: N:T.21, N:V.31, N:V.31, N:K.33, N:A.49, N:A.52, H:D.124, H:A.126, H:N.130
- Hydrogen bonds: N:T.1, N:T.21, N:T.21, N:Q.22, N:S.27, N:G.47, N:A.49, H:D.124
- Water bridges: N:T.1, N:A.50
U5Y.21: 20 residues within 4Å:- Chain V: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain W: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.22
15 PLIP interactions:12 interactions with chain V, 3 interactions with chain W- Hydrophobic interactions: V:V.31, V:V.31, V:K.33, V:A.49, V:A.52, W:D.124, W:N.130
- Hydrogen bonds: V:T.21, V:T.21, V:Q.22, V:S.27, V:G.47, V:A.49, W:D.124
- Water bridges: V:A.50
U5Y.24: 21 residues within 4Å:- Chain W: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain X: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.25
19 PLIP interactions:16 interactions with chain W, 3 interactions with chain X- Hydrophobic interactions: W:V.31, W:V.31, W:K.33, W:K.33, W:A.49, W:A.52, W:V.53, X:D.124, X:N.130
- Hydrogen bonds: W:T.1, W:T.21, W:T.21, W:Q.22, W:S.27, W:G.47, W:A.49, X:D.124
- Water bridges: W:G.23, W:A.50
U5Y.27: 23 residues within 4Å:- Chain X: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, G.97
- Chain Y: S.122, F.123, D.124, A.126, G.128, W.129, N.130
- Ligands: DMF.26, CIT.28
17 PLIP interactions:13 interactions with chain X, 4 interactions with chain Y- Hydrophobic interactions: X:V.31, X:V.31, X:K.33, X:K.33, X:A.49, X:A.52, Y:A.126, Y:N.130
- Hydrogen bonds: X:T.1, X:T.21, X:T.21, X:S.27, X:G.47, X:A.49, Y:D.124, Y:D.124
- Water bridges: X:A.50
U5Y.29: 21 residues within 4Å:- Chain Y: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, G.97
- Chain Z: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.30
17 PLIP interactions:14 interactions with chain Y, 3 interactions with chain Z- Hydrophobic interactions: Y:V.31, Y:V.31, Y:K.33, Y:K.33, Y:A.49, Y:A.52, Z:D.124
- Hydrogen bonds: Y:T.1, Y:T.21, Y:T.21, Y:Q.22, Y:S.27, Y:G.47, Y:A.49, Z:D.124, Z:D.124
- Water bridges: Y:A.50
U5Y.31: 22 residues within 4Å:- Chain 0: S.122, F.123, D.124, A.126, G.128, W.129, N.130
- Chain Z: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, G.97
- Ligands: CIT.32
16 PLIP interactions:11 interactions with chain Z, 5 interactions with chain 0- Hydrophobic interactions: Z:V.31, Z:K.33, Z:K.33, Z:A.49, Z:A.52, 0:D.124, 0:A.126, 0:N.130
- Hydrogen bonds: Z:T.21, Z:T.21, Z:Q.22, Z:S.27, Z:G.47, Z:A.49, 0:D.124, 0:D.124
U5Y.33: 20 residues within 4Å:- Chain 0: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain 1: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.34
13 PLIP interactions:11 interactions with chain 0, 2 interactions with chain 1- Hydrophobic interactions: 0:V.31, 0:V.31, 0:K.33, 0:K.33, 0:A.49, 0:A.52, 1:D.124
- Hydrogen bonds: 0:T.21, 0:T.21, 0:S.27, 0:G.47, 0:A.49, 1:D.124
U5Y.35: 20 residues within 4Å:- Chain 1: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52
- Chain V: S.122, F.123, D.124, G.128, W.129, N.130
- Ligands: CIT.36
17 PLIP interactions:14 interactions with chain 1, 3 interactions with chain V- Hydrophobic interactions: 1:V.31, 1:V.31, 1:K.33, 1:K.33, 1:A.49, 1:A.52, V:D.124, V:N.130
- Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:Q.22, 1:S.27, 1:G.47, 1:A.49, V:D.124
- Water bridges: 1:A.50
- 14 x CIT: CITRIC ACID(Non-functional Binders)
CIT.2: 7 residues within 4Å:- Chain H: T.1, A.46, G.47, L.101, G.140, S.141
- Ligands: U5Y.1
7 PLIP interactions:7 interactions with chain H- Hydrophobic interactions: H:A.46
- Hydrogen bonds: H:T.1, H:T.1, H:G.47, H:S.141
- Water bridges: H:G.140
- Salt bridges: H:K.33
CIT.4: 8 residues within 4Å:- Chain I: T.1, A.46, G.47, L.99, G.140, S.141, A.180
- Ligands: U5Y.3
7 PLIP interactions:6 interactions with chain I, 1 interactions with chain X- Hydrophobic interactions: I:A.180
- Hydrogen bonds: I:T.1, I:G.47, I:S.141, X:N.24
- Water bridges: I:A.180
- Salt bridges: I:K.33
CIT.6: 6 residues within 4Å:- Chain J: T.1, A.46, G.47, G.140, S.141
- Ligands: U5Y.5
8 PLIP interactions:8 interactions with chain J- Hydrophobic interactions: J:A.46
- Hydrogen bonds: J:T.1, J:T.1, J:G.47, J:S.141
- Water bridges: J:T.21, J:G.140
- Salt bridges: J:K.33
CIT.8: 6 residues within 4Å:- Chain K: T.1, A.46, G.47, G.140, S.141
- Ligands: U5Y.7
9 PLIP interactions:8 interactions with chain K, 1 interactions with chain V- Hydrophobic interactions: K:A.46
- Hydrogen bonds: K:T.1, K:T.1, K:G.47, K:S.141, V:N.24
- Water bridges: K:T.21, K:G.140
- Salt bridges: K:K.33
CIT.10: 9 residues within 4Å:- Chain 1: N.24
- Chain L: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: U5Y.9
8 PLIP interactions:7 interactions with chain L, 1 interactions with chain 1- Hydrophobic interactions: L:A.46
- Hydrogen bonds: L:T.1, L:T.1, L:G.47, L:S.141, L:S.141, 1:N.24
- Salt bridges: L:K.33
CIT.12: 9 residues within 4Å:- Chain 0: N.24
- Chain M: T.1, A.46, G.47, L.99, G.140, S.141, A.180
- Ligands: U5Y.11
8 PLIP interactions:7 interactions with chain M, 1 interactions with chain 0- Hydrophobic interactions: M:A.46
- Hydrogen bonds: M:T.1, M:T.1, M:G.47, M:S.141, M:S.141, 0:N.24
- Salt bridges: M:K.33
CIT.14: 9 residues within 4Å:- Chain N: T.1, T.21, A.46, G.47, L.101, S.141, A.180
- Chain Z: N.24
- Ligands: U5Y.13
10 PLIP interactions:9 interactions with chain N, 1 interactions with chain Z- Hydrophobic interactions: N:A.46
- Hydrogen bonds: N:T.1, N:T.1, N:G.47, N:S.141, N:S.141, Z:N.24
- Water bridges: N:T.1, N:A.180
- Salt bridges: N:K.33
CIT.22: 9 residues within 4Å:- Chain K: N.24
- Chain V: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: U5Y.21
11 PLIP interactions:11 interactions with chain V- Hydrophobic interactions: V:A.46
- Hydrogen bonds: V:T.1, V:T.1, V:T.21, V:T.21, V:G.47, V:S.141, V:S.141
- Water bridges: V:T.21, V:T.21
- Salt bridges: V:K.33
CIT.25: 6 residues within 4Å:- Chain W: T.1, A.46, G.47, G.140, S.141
- Ligands: U5Y.24
7 PLIP interactions:7 interactions with chain W- Hydrophobic interactions: W:A.46
- Hydrogen bonds: W:T.1, W:T.1, W:G.47, W:G.47, W:S.141
- Salt bridges: W:K.33
CIT.28: 7 residues within 4Å:- Chain X: T.1, A.46, G.47, G.140, S.141
- Ligands: DMF.26, U5Y.27
7 PLIP interactions:7 interactions with chain X- Hydrophobic interactions: X:A.46
- Hydrogen bonds: X:T.1, X:T.1, X:G.47, X:G.47, X:S.141
- Salt bridges: X:K.33
CIT.30: 10 residues within 4Å:- Chain H: N.24
- Chain Y: T.1, T.21, A.46, G.47, L.99, G.140, S.141, A.180
- Ligands: U5Y.29
9 PLIP interactions:8 interactions with chain Y, 1 interactions with chain H- Hydrogen bonds: Y:T.1, Y:T.1, Y:G.47, Y:S.141, H:N.24
- Water bridges: Y:T.21, Y:T.21, Y:A.180
- Salt bridges: Y:K.33
CIT.32: 8 residues within 4Å:- Chain N: N.24
- Chain Z: T.1, A.46, G.47, L.99, G.140, S.141
- Ligands: U5Y.31
7 PLIP interactions:6 interactions with chain Z, 1 interactions with chain N- Hydrophobic interactions: Z:A.46
- Hydrogen bonds: Z:T.1, Z:T.1, Z:G.47, Z:S.141, N:N.24
- Salt bridges: Z:K.33
CIT.34: 8 residues within 4Å:- Chain 0: T.1, A.46, G.47, G.140, S.141, A.180
- Chain M: N.24
- Ligands: U5Y.33
9 PLIP interactions:8 interactions with chain 0, 1 interactions with chain M- Hydrogen bonds: 0:T.1, 0:T.1, 0:T.21, 0:G.47, 0:S.141, 0:S.141, M:N.24
- Water bridges: 0:T.21
- Salt bridges: 0:K.33
CIT.36: 8 residues within 4Å:- Chain 1: T.1, A.46, G.47, G.140, S.141, A.180
- Chain L: N.24
- Ligands: U5Y.35
7 PLIP interactions:6 interactions with chain 1, 1 interactions with chain L- Hydrogen bonds: 1:T.1, 1:T.1, 1:G.47, 1:G.47, 1:S.141, L:N.24
- Salt bridges: 1:K.33
- 8 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
DMF.15: 4 residues within 4Å:- Chain O: G.69, G.70, V.94, T.98
No protein-ligand interaction detected (PLIP)DMF.16: 4 residues within 4Å:- Chain P: G.69, V.94, Y.95, T.98
2 PLIP interactions:2 interactions with chain P- Hydrogen bonds: P:T.98
- Water bridges: P:F.73
DMF.17: 6 residues within 4Å:- Chain Q: L.66, G.69, G.70, V.94, Y.95, T.98
1 PLIP interactions:1 interactions with chain Q- Hydrogen bonds: Q:T.98
DMF.18: 8 residues within 4Å:- Chain R: Y.27, A.28, G.30, V.119, A.120, K.126, P.128, A.207
No protein-ligand interaction detected (PLIP)DMF.19: 10 residues within 4Å:- Chain Q: R.89, N.93
- Chain R: S.41, L.42, Q.43, F.60, D.64, R.67, R.68
- Chain Y: L.69
4 PLIP interactions:1 interactions with chain R, 3 interactions with chain Q- Water bridges: R:R.68
- Hydrogen bonds: Q:R.89, Q:R.89, Q:N.93
DMF.20: 4 residues within 4Å:- Chain S: N.65, G.69, G.70, T.98
No protein-ligand interaction detected (PLIP)DMF.23: 5 residues within 4Å:- Chain O: D.82
- Chain V: R.57
- Chain W: A.77, I.80, W.129
No protein-ligand interaction detected (PLIP)DMF.26: 4 residues within 4Å:- Chain X: T.21, G.23
- Ligands: U5Y.27, CIT.28
1 PLIP interactions:1 interactions with chain X- Hydrogen bonds: X:G.23
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, H. et al., Macrocyclic Peptides that Selectively Inhibit the Mycobacterium tuberculosis Proteasome. J.Med.Chem. (2021)
- Release Date
- 2021-04-28
- Peptides
- Proteasome subunit alpha: ABCDEFGOPQRSTU
Proteasome subunit beta: HIJKLMNVWXYZ01 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GO
OP
PQ
QR
RS
ST
TU
UH
HI
IJ
JK
KL
LM
MN
NV
VW
WX
XY
YZ
Z0
a1
b
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.28 Å
- Oligo State
- hetero-14-14-mer
- Ligands
- 14 x U5Y: (12S,15S)-N-[(2-fluorophenyl)methyl]-10,13-dioxo-12-{2-oxo-2-[(2R)-2-phenylpyrrolidin-1-yl]ethyl}-2-oxa-11,14-diazatricyclo[15.2.2.1~3,7~]docosa-1(19),3(22),4,6,17,20-hexaene-15-carboxamide(Non-covalent)
- 14 x CIT: CITRIC ACID(Non-functional Binders)
- 8 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhang, H. et al., Macrocyclic Peptides that Selectively Inhibit the Mycobacterium tuberculosis Proteasome. J.Med.Chem. (2021)
- Release Date
- 2021-04-28
- Peptides
- Proteasome subunit alpha: ABCDEFGOPQRSTU
Proteasome subunit beta: HIJKLMNVWXYZ01 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GO
OP
PQ
QR
RS
ST
TU
UH
HI
IJ
JK
KL
LM
MN
NV
VW
WX
XY
YZ
Z0
a1
b