- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x 420: N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE(Covalent)
- 12 x COA: COENZYME A(Non-covalent)
COA.2: 17 residues within 4Å:- Chain A: R.28, T.32, M.33, R.34, F.64, R.65, E.67
- Chain J: R.6, I.8, T.32, M.33, F.64, L.66
- Chain L: R.6, L.66
- Ligands: COA.37, COA.45
9 PLIP interactions:7 interactions with chain A, 1 interactions with chain J, 1 interactions with chain L- Hydrogen bonds: A:R.34, A:R.34, A:R.34, A:R.65, A:E.67, L:R.6
- Salt bridges: A:R.28
- pi-Cation interactions: A:R.34
- Hydrophobic interactions: J:L.66
COA.6: 21 residues within 4Å:- Chain B: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain C: R.6, I.8, R.28, A.29, T.32, M.33, F.64, L.66
- Chain E: R.6, L.66
- Ligands: CL.9, COA.11, COA.18
10 PLIP interactions:8 interactions with chain B, 1 interactions with chain E, 1 interactions with chain C- Hydrogen bonds: B:T.32, B:R.34, B:R.34, B:R.34, B:R.65, B:E.67, E:R.6
- Salt bridges: B:R.28
- pi-Cation interactions: B:R.34
- Hydrophobic interactions: C:L.66
COA.11: 21 residues within 4Å:- Chain B: R.6, L.66
- Chain C: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain E: R.6, I.8, R.28, A.29, T.32, M.33, F.64, L.66
- Ligands: COA.6, CL.9, COA.18
10 PLIP interactions:8 interactions with chain C, 1 interactions with chain E, 1 interactions with chain B- Hydrogen bonds: C:R.34, C:R.34, C:R.34, C:R.65, C:E.67, C:E.67, B:R.6
- Salt bridges: C:R.28
- pi-Cation interactions: C:R.34
- Hydrophobic interactions: E:L.66
COA.14: 18 residues within 4Å:- Chain D: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain F: R.6, I.8, A.29, M.33, F.64, L.66
- Chain G: R.6, L.66
- Ligands: COA.22, COA.25
11 PLIP interactions:7 interactions with chain D, 3 interactions with chain F, 1 interactions with chain G- Hydrogen bonds: D:T.32, D:R.34, D:R.34, D:R.65, D:E.67, G:R.6
- Salt bridges: D:R.28
- pi-Cation interactions: D:R.34
- Hydrophobic interactions: F:I.8, F:F.64, F:L.66
COA.18: 20 residues within 4Å:- Chain B: R.6, I.8, A.29, T.32, M.33, F.64, L.66
- Chain C: R.6, L.66
- Chain E: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Ligands: COA.6, CL.9, COA.11
12 PLIP interactions:8 interactions with chain E, 3 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: E:T.32, E:R.34, E:R.34, E:R.34, E:R.65, E:E.67, B:R.6, C:R.6
- Salt bridges: E:R.28
- pi-Cation interactions: E:R.34
- Hydrophobic interactions: B:F.64, B:L.66
COA.22: 18 residues within 4Å:- Chain D: R.6, L.66
- Chain F: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain G: R.6, I.8, T.32, M.33, F.64, L.66
- Ligands: COA.14, COA.25
11 PLIP interactions:3 interactions with chain G, 7 interactions with chain F, 1 interactions with chain D- Hydrophobic interactions: G:F.64, G:L.66
- Hydrogen bonds: G:R.6, F:R.34, F:R.34, F:R.34, F:R.65, F:E.67, D:R.6
- Salt bridges: F:R.28
- pi-Cation interactions: F:R.34
COA.25: 17 residues within 4Å:- Chain D: R.6, I.8, T.32, M.33, F.64, L.66
- Chain F: R.6, L.66
- Chain G: R.28, T.32, M.33, R.34, F.64, R.65, E.67
- Ligands: COA.14, COA.22
11 PLIP interactions:9 interactions with chain G, 1 interactions with chain D, 1 interactions with chain F- Hydrogen bonds: G:T.32, G:R.34, G:R.34, G:R.34, G:R.65, G:E.67, G:E.67, F:R.6
- Salt bridges: G:R.28
- pi-Cation interactions: G:R.34
- Hydrophobic interactions: D:L.66
COA.29: 21 residues within 4Å:- Chain H: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain I: R.6, I.8, R.28, A.29, T.32, M.33, F.64, L.66
- Chain K: R.6, L.66
- Ligands: CL.32, COA.34, COA.41
10 PLIP interactions:8 interactions with chain H, 1 interactions with chain K, 1 interactions with chain I- Hydrogen bonds: H:R.34, H:R.34, H:R.34, H:R.65, H:E.67, H:E.67, K:R.6
- Salt bridges: H:R.28
- pi-Cation interactions: H:R.34
- Hydrophobic interactions: I:L.66
COA.34: 21 residues within 4Å:- Chain H: R.6, L.66
- Chain I: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain K: R.6, I.8, R.28, A.29, T.32, M.33, F.64, L.66
- Ligands: COA.29, CL.32, COA.41
10 PLIP interactions:8 interactions with chain I, 1 interactions with chain H, 1 interactions with chain K- Hydrogen bonds: I:T.32, I:R.34, I:R.34, I:R.34, I:R.65, I:E.67, H:R.6
- Salt bridges: I:R.28
- pi-Cation interactions: I:R.34
- Hydrophobic interactions: K:L.66
COA.37: 18 residues within 4Å:- Chain A: R.6, L.66
- Chain J: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Chain L: R.6, I.8, A.29, M.33, F.64, L.66
- Ligands: COA.2, COA.45
10 PLIP interactions:6 interactions with chain J, 1 interactions with chain A, 3 interactions with chain L- Hydrogen bonds: J:R.34, J:R.34, J:R.65, J:E.67, A:R.6
- Salt bridges: J:R.28
- pi-Cation interactions: J:R.34
- Hydrophobic interactions: L:I.8, L:F.64, L:L.66
COA.41: 20 residues within 4Å:- Chain H: R.6, I.8, A.29, T.32, M.33, F.64, L.66
- Chain I: R.6, L.66
- Chain K: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Ligands: COA.29, CL.32, COA.34
12 PLIP interactions:8 interactions with chain K, 3 interactions with chain H, 1 interactions with chain I- Hydrogen bonds: K:R.34, K:R.34, K:R.34, K:R.65, K:E.67, K:E.67, H:R.6, I:R.6
- Salt bridges: K:R.28
- pi-Cation interactions: K:R.34
- Hydrophobic interactions: H:F.64, H:L.66
COA.45: 18 residues within 4Å:- Chain A: R.6, I.8, T.32, M.33, F.64, L.66
- Chain J: R.6, L.66
- Chain L: R.28, T.32, M.33, R.34, F.64, R.65, L.66, E.67
- Ligands: COA.2, COA.37
13 PLIP interactions:9 interactions with chain L, 1 interactions with chain J, 3 interactions with chain A- Hydrogen bonds: L:T.32, L:R.34, L:R.34, L:R.34, L:R.65, L:E.67, L:E.67, J:R.6, A:R.6
- Salt bridges: L:R.28
- pi-Cation interactions: L:R.34
- Hydrophobic interactions: A:F.64, A:L.66
- 12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
FMN.3: 13 residues within 4Å:- Chain A: Y.5, D.37, W.38, R.65
- Chain B: R.45, H.47, Q.57
- Chain L: V.11, R.45, Q.57
- Ligands: 420.5, FMN.12, 420.44
13 PLIP interactions:6 interactions with chain A, 4 interactions with chain L, 3 interactions with chain B- Hydrogen bonds: A:Y.5, A:D.37, A:D.37, B:R.45, B:Q.57, B:Q.57
- Salt bridges: A:R.65
- pi-Stacking: A:W.38, A:W.38
- Hydrophobic interactions: L:V.11, L:Q.57
- Water bridges: L:H.47, L:H.47
FMN.7: 14 residues within 4Å:- Chain B: H.3, Y.5, D.37, W.38, R.65
- Chain D: R.45, H.47, Q.57
- Chain E: V.11, R.45, Q.57
- Ligands: 420.13, 420.17, FMN.23
13 PLIP interactions:8 interactions with chain B, 4 interactions with chain D, 1 interactions with chain E- Hydrophobic interactions: B:W.38, E:Q.57
- Hydrogen bonds: B:Y.5, B:D.37, B:D.37, D:R.45, D:H.47, D:Q.57, D:Q.57
- Salt bridges: B:R.65
- pi-Stacking: B:W.38, B:W.38, B:W.38
FMN.12: 13 residues within 4Å:- Chain B: V.11, Q.57
- Chain C: H.3, Y.5, D.37, W.38, R.65
- Chain L: R.45, H.47, Q.57
- Ligands: FMN.3, 420.5, 420.44
13 PLIP interactions:7 interactions with chain C, 3 interactions with chain B, 3 interactions with chain L- Hydrophobic interactions: C:W.38, C:W.38, B:V.11, B:V.11, B:Q.57
- Hydrogen bonds: C:Y.5, C:D.37, L:R.45, L:Q.57, L:Q.57
- Salt bridges: C:R.65
- pi-Stacking: C:W.38, C:W.38
FMN.15: 13 residues within 4Å:- Chain A: R.45, G.46, H.47, Q.57
- Chain D: Y.5, D.37, W.38, R.65
- Chain G: V.11, Q.57
- Ligands: 420.1, 420.24, FMN.38
15 PLIP interactions:3 interactions with chain G, 4 interactions with chain A, 8 interactions with chain D- Hydrophobic interactions: G:V.11, G:V.11, G:Q.57, D:W.38
- Hydrogen bonds: A:R.45, A:H.47, A:Q.57, A:Q.57, D:Y.5, D:D.37, D:D.37, D:D.37
- Salt bridges: D:R.65
- pi-Stacking: D:W.38, D:W.38
FMN.19: 13 residues within 4Å:- Chain C: V.11, R.45, Q.57
- Chain E: Y.5, D.37, W.38
- Chain I: R.45, G.46, H.47, Q.57
- Ligands: 420.10, 420.33, FMN.42
10 PLIP interactions:3 interactions with chain I, 5 interactions with chain E, 2 interactions with chain C- Hydrogen bonds: I:R.45, I:Q.57, I:Q.57, E:Y.5, E:D.37
- Salt bridges: E:R.65
- pi-Stacking: E:W.38, E:W.38
- Hydrophobic interactions: C:V.11, C:Q.57
FMN.23: 14 residues within 4Å:- Chain D: V.11, R.45, Q.57
- Chain E: R.45, H.47, Q.57
- Chain F: H.3, Y.5, D.37, W.38, R.65
- Ligands: FMN.7, 420.13, 420.17
10 PLIP interactions:4 interactions with chain E, 2 interactions with chain D, 4 interactions with chain F- Hydrogen bonds: E:R.45, E:H.47, E:Q.57, E:Q.57
- Hydrophobic interactions: D:V.11, D:Q.57
- Salt bridges: F:H.3, F:R.65
- pi-Stacking: F:W.38, F:W.38
FMN.26: 13 residues within 4Å:- Chain F: V.11, R.45, Q.57
- Chain G: Y.5, D.37, W.38, R.65
- Chain H: R.45, H.47, Q.57
- Ligands: 420.21, 420.28, FMN.35
10 PLIP interactions:3 interactions with chain F, 3 interactions with chain H, 4 interactions with chain G- Hydrophobic interactions: F:V.11, F:Q.57
- Water bridges: F:H.47
- Hydrogen bonds: H:R.45, H:Q.57, H:Q.57, G:D.37
- Salt bridges: G:R.65
- pi-Stacking: G:W.38, G:W.38
FMN.30: 14 residues within 4Å:- Chain H: H.3, Y.5, D.37, W.38, R.65
- Chain J: R.45, H.47, Q.57
- Chain K: V.11, R.45, Q.57
- Ligands: 420.36, 420.40, FMN.46
11 PLIP interactions:4 interactions with chain J, 6 interactions with chain H, 1 interactions with chain K- Hydrogen bonds: J:R.45, J:H.47, J:Q.57, J:Q.57, H:D.37
- Hydrophobic interactions: H:W.38, K:Q.57
- Salt bridges: H:R.65
- pi-Stacking: H:W.38, H:W.38, H:W.38
FMN.35: 13 residues within 4Å:- Chain F: R.45, H.47, Q.57
- Chain H: V.11, Q.57
- Chain I: H.3, Y.5, D.37, W.38, R.65
- Ligands: 420.21, FMN.26, 420.28
13 PLIP interactions:4 interactions with chain F, 6 interactions with chain I, 3 interactions with chain H- Hydrogen bonds: F:R.45, F:H.47, F:Q.57, F:Q.57, I:D.37
- Hydrophobic interactions: I:W.38, I:W.38, H:V.11, H:V.11, H:Q.57
- Salt bridges: I:R.65
- pi-Stacking: I:W.38, I:W.38
FMN.38: 13 residues within 4Å:- Chain A: V.11, Q.57
- Chain G: R.45, G.46, H.47, Q.57
- Chain J: Y.5, D.37, W.38, R.65
- Ligands: 420.1, FMN.15, 420.24
12 PLIP interactions:3 interactions with chain A, 6 interactions with chain J, 3 interactions with chain G- Hydrophobic interactions: A:V.11, A:V.11, A:Q.57, J:W.38
- Hydrogen bonds: J:D.37, J:D.37, G:R.45, G:Q.57, G:Q.57
- Salt bridges: J:R.65
- pi-Stacking: J:W.38, J:W.38
FMN.42: 13 residues within 4Å:- Chain C: R.45, G.46, H.47, Q.57
- Chain I: V.11, R.45, Q.57
- Chain K: Y.5, D.37, W.38
- Ligands: 420.10, FMN.19, 420.33
10 PLIP interactions:4 interactions with chain C, 4 interactions with chain K, 2 interactions with chain I- Hydrogen bonds: C:R.45, C:H.47, C:Q.57, C:Q.57, K:D.37
- Salt bridges: K:R.65
- pi-Stacking: K:W.38, K:W.38
- Hydrophobic interactions: I:V.11, I:Q.57
FMN.46: 14 residues within 4Å:- Chain J: V.11, R.45, Q.57
- Chain K: R.45, H.47, Q.57
- Chain L: H.3, Y.5, D.37, W.38, R.65
- Ligands: FMN.30, 420.36, 420.40
11 PLIP interactions:2 interactions with chain J, 4 interactions with chain K, 5 interactions with chain L- Hydrophobic interactions: J:V.11, J:Q.57
- Hydrogen bonds: K:R.45, K:H.47, K:Q.57, K:Q.57, L:Y.5
- Salt bridges: L:H.3, L:R.65
- pi-Stacking: L:W.38, L:W.38
- 6 x CL: CHLORIDE ION(Non-functional Binders)
CL.4: 2 residues within 4Å:- Chain J: K.61
- Chain L: K.61
Ligand excluded by PLIPCL.8: 3 residues within 4Å:- Chain B: K.61
- Chain C: K.61
- Chain E: K.61
Ligand excluded by PLIPCL.9: 3 residues within 4Å:- Ligands: COA.6, COA.11, COA.18
Ligand excluded by PLIPCL.27: 2 residues within 4Å:- Chain D: K.61
- Chain F: K.61
Ligand excluded by PLIPCL.31: 3 residues within 4Å:- Chain H: K.61
- Chain I: K.61
- Chain K: K.61
Ligand excluded by PLIPCL.32: 3 residues within 4Å:- Ligands: COA.29, COA.34, COA.41
Ligand excluded by PLIP- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.16: 12 residues within 4Å:- Chain D: R.6, V.7, I.8, E.9
- Chain F: R.6, V.7, I.8, E.9
- Chain G: R.6, V.7, I.8, E.9
8 PLIP interactions:2 interactions with chain G, 3 interactions with chain D, 3 interactions with chain F- Hydrogen bonds: G:E.9, D:V.7, D:E.9, F:E.9
- Salt bridges: G:R.6, D:R.6, F:R.6
- Water bridges: F:V.7
SO4.20: 12 residues within 4Å:- Chain B: R.6, V.7, I.8, E.9
- Chain C: R.6, V.7, I.8, E.9
- Chain E: R.6, V.7, I.8, E.9
9 PLIP interactions:3 interactions with chain C, 3 interactions with chain B, 3 interactions with chain E- Hydrogen bonds: C:V.7, C:E.9, B:E.9, E:V.7, E:E.9
- Salt bridges: C:R.6, B:R.6, E:R.6
- Water bridges: B:E.9
SO4.39: 12 residues within 4Å:- Chain A: R.6, V.7, I.8, E.9
- Chain J: R.6, V.7, I.8, E.9
- Chain L: R.6, V.7, I.8, E.9
12 PLIP interactions:3 interactions with chain J, 6 interactions with chain A, 3 interactions with chain L- Hydrogen bonds: J:V.7, J:E.9, A:E.9, L:E.9
- Salt bridges: J:R.6, A:R.6, L:R.6
- Water bridges: A:E.9, A:E.9, A:E.9, A:E.9, L:V.7
SO4.43: 12 residues within 4Å:- Chain H: R.6, V.7, I.8, E.9
- Chain I: R.6, V.7, I.8, E.9
- Chain K: R.6, V.7, I.8, E.9
9 PLIP interactions:2 interactions with chain H, 3 interactions with chain K, 4 interactions with chain I- Hydrogen bonds: H:E.9, K:V.7, K:E.9, I:V.7, I:E.9
- Salt bridges: H:R.6, K:R.6, I:R.6
- Water bridges: I:E.9
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vinzenz, X. et al., Chemical Engineering of Mycobacterium Tuberculosis Dodecin Hybrids. Chem.Commun.(Camb.) (2011)
- Release Date
- 2011-10-12
- Peptides
- DODECIN: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
AH
BI
CJ
DK
EL
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x 420: N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE(Covalent)
- 12 x COA: COENZYME A(Non-covalent)
- 12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
- 6 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vinzenz, X. et al., Chemical Engineering of Mycobacterium Tuberculosis Dodecin Hybrids. Chem.Commun.(Camb.) (2011)
- Release Date
- 2011-10-12
- Peptides
- DODECIN: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
AH
BI
CJ
DK
EL
F