- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-12-mer
- Ligands
- 3 x LYS- THR- THR- CYS- ASN- ALA- CYS- HIS- GLN: Heme-Peptide Fragment(Non-covalent)
- 15 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
HEM.2: 18 residues within 4Å:- Chain A: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106
17 PLIP interactions:17 interactions with chain A,- Hydrophobic interactions: A:M.7, A:L.10, A:L.10, A:N.11, A:L.14, A:P.45, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106
- Hydrogen bonds: A:E.4
- Water bridges: A:R.106, A:R.106, A:R.106
- pi-Cation interactions: A:R.106
- Metal complexes: A:H.102
HEM.7: 17 residues within 4Å:- Chain B: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:M.7, B:L.10, B:N.11, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106
- Water bridges: B:E.4, B:E.4
- pi-Cation interactions: B:R.106
- Metal complexes: B:H.102
HEM.14: 18 residues within 4Å:- Chain C: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:M.7, C:N.11, C:L.14, C:P.45, C:F.65, C:F.65, C:F.65, C:L.68, C:R.106
- pi-Stacking: C:H.102, C:H.102
- Metal complexes: C:H.102
HEM.16: 17 residues within 4Å:- Chain D: L.3, E.4, M.7, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106
11 PLIP interactions:11 interactions with chain D,- Hydrophobic interactions: D:M.7, D:N.11, D:L.14, D:P.45, D:F.65, D:F.65, D:F.65, D:R.106
- Hydrogen bonds: D:E.4
- pi-Cation interactions: D:R.106
- Metal complexes: D:H.102
HEM.20: 17 residues within 4Å:- Chain B: T.31, A.34, A.38, W.66, I.69, H.73, L.76, N.80
- Chain G: A.38, D.39, W.41, W.66, I.69
- Ligands: LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.1, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.1, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.1, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.1
13 PLIP interactions:4 interactions with chain G, 9 interactions with chain B,- Hydrophobic interactions: G:D.39, G:W.41, G:W.66, G:I.69, B:T.31, B:A.38, B:W.66, B:I.69, B:L.76
- Hydrogen bonds: B:N.80
- Salt bridges: B:K.27
- pi-Stacking: B:H.73
- Metal complexes: B:H.73
HEM.22: 18 residues within 4Å:- Chain E: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106
17 PLIP interactions:17 interactions with chain E,- Hydrophobic interactions: E:M.7, E:L.10, E:L.10, E:N.11, E:L.14, E:P.45, E:F.65, E:F.65, E:F.65, E:L.68, E:R.106
- Hydrogen bonds: E:E.4
- Water bridges: E:R.106, E:R.106, E:R.106
- pi-Cation interactions: E:R.106
- Metal complexes: E:H.102
HEM.27: 17 residues within 4Å:- Chain F: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106
15 PLIP interactions:15 interactions with chain F,- Hydrophobic interactions: F:M.7, F:L.10, F:N.11, F:L.14, F:P.45, F:F.61, F:F.65, F:F.65, F:F.65, F:L.68, F:R.106
- Water bridges: F:E.4, F:E.4
- pi-Cation interactions: F:R.106
- Metal complexes: F:H.102
HEM.34: 18 residues within 4Å:- Chain G: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106
11 PLIP interactions:11 interactions with chain G,- Hydrophobic interactions: G:M.7, G:N.11, G:L.14, G:P.45, G:F.65, G:F.65, G:F.65, G:L.68, G:R.106
- pi-Stacking: G:H.102
- Metal complexes: G:H.102
HEM.36: 17 residues within 4Å:- Chain H: L.3, E.4, M.7, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106
11 PLIP interactions:11 interactions with chain H,- Hydrophobic interactions: H:M.7, H:N.11, H:L.14, H:P.45, H:F.65, H:F.65, H:F.65, H:R.106
- Hydrogen bonds: H:E.4
- pi-Cation interactions: H:R.106
- Metal complexes: H:H.102
HEM.40: 17 residues within 4Å:- Chain F: T.31, A.34, A.38, W.66, I.69, H.73, L.76, N.80
- Chain K: A.38, D.39, W.41, W.66, I.69
- Ligands: LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.21, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.21, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.21, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.21
13 PLIP interactions:9 interactions with chain F, 4 interactions with chain K,- Hydrophobic interactions: F:T.31, F:A.38, F:W.66, F:I.69, F:L.76, K:D.39, K:W.41, K:W.66, K:I.69
- Hydrogen bonds: F:N.80
- Salt bridges: F:K.27
- pi-Stacking: F:H.73
- Metal complexes: F:H.73
HEM.42: 18 residues within 4Å:- Chain I: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106
17 PLIP interactions:17 interactions with chain I,- Hydrophobic interactions: I:M.7, I:L.10, I:L.10, I:N.11, I:L.14, I:P.45, I:F.65, I:F.65, I:F.65, I:L.68, I:R.106
- Hydrogen bonds: I:E.4
- Water bridges: I:R.106, I:R.106, I:R.106
- pi-Cation interactions: I:R.106
- Metal complexes: I:H.102
HEM.47: 17 residues within 4Å:- Chain J: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106
15 PLIP interactions:15 interactions with chain J,- Hydrophobic interactions: J:M.7, J:L.10, J:N.11, J:L.14, J:P.45, J:F.61, J:F.65, J:F.65, J:F.65, J:L.68, J:R.106
- Water bridges: J:E.4, J:E.4
- pi-Cation interactions: J:R.106
- Metal complexes: J:H.102
HEM.54: 18 residues within 4Å:- Chain K: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106
11 PLIP interactions:11 interactions with chain K,- Hydrophobic interactions: K:M.7, K:N.11, K:L.14, K:P.45, K:F.65, K:F.65, K:F.65, K:L.68, K:R.106
- pi-Stacking: K:H.102
- Metal complexes: K:H.102
HEM.56: 17 residues within 4Å:- Chain L: L.3, E.4, M.7, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106
11 PLIP interactions:11 interactions with chain L,- Hydrophobic interactions: L:M.7, L:N.11, L:L.14, L:P.45, L:F.65, L:F.65, L:F.65, L:R.106
- Hydrogen bonds: L:E.4
- pi-Cation interactions: L:R.106
- Metal complexes: L:H.102
HEM.60: 17 residues within 4Å:- Chain C: A.38, D.39, W.41, W.66, I.69
- Chain J: T.31, A.34, A.38, W.66, I.69, H.73, L.76, N.80
- Ligands: LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.41, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.41, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.41, LYS-THR-THR-CYS-ASN-ALA-CYS-HIS-GLN.41
13 PLIP interactions:4 interactions with chain C, 9 interactions with chain J,- Hydrophobic interactions: C:D.39, C:W.41, C:W.66, C:I.69, J:T.31, J:A.38, J:W.66, J:I.69, J:L.76
- Hydrogen bonds: J:N.80
- Salt bridges: J:K.27
- pi-Stacking: J:H.73
- Metal complexes: J:H.73
- 12 x ACT: ACETATE ION(Non-functional Binders)
ACT.3: 7 residues within 4Å:- Chain A: H.63, C.67
- Chain I: P.53, D.54, H.59, R.62
- Ligands: ZN.46
4 PLIP interactions:3 interactions with chain I, 1 interactions with chain A- Water bridges: I:R.62
- Salt bridges: I:H.59, I:R.62, A:H.63
ACT.8: 7 residues within 4Å:- Chain B: H.63, C.67
- Chain G: P.53, D.54, H.59, R.62
- Ligands: ZN.12
4 PLIP interactions:1 interactions with chain B, 3 interactions with chain G- Salt bridges: B:H.63, G:H.59, G:R.62
- Water bridges: G:R.62
ACT.15: 7 residues within 4Å:- Chain C: H.63, C.67
- Chain D: P.53, D.54, H.59, R.62
- Ligands: ZN.18
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:D.54
- Water bridges: D:R.62, D:R.62
- Salt bridges: D:H.59, D:R.62, C:H.63
ACT.17: 7 residues within 4Å:- Chain D: H.63, C.67
- Chain J: P.53, D.54, H.59, R.62
- Ligands: ZN.51
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain J- Water bridges: D:H.63, J:R.62
- Salt bridges: D:H.63, J:H.59, J:R.62
ACT.23: 7 residues within 4Å:- Chain A: P.53, D.54, H.59, R.62
- Chain E: H.63, C.67
- Ligands: ZN.6
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain E- Water bridges: A:R.62
- Salt bridges: A:H.59, A:R.62, E:H.63
ACT.28: 7 residues within 4Å:- Chain F: H.63, C.67
- Chain K: P.53, D.54, H.59, R.62
- Ligands: ZN.32
4 PLIP interactions:3 interactions with chain K, 1 interactions with chain F- Water bridges: K:R.62
- Salt bridges: K:H.59, K:R.62, F:H.63
ACT.35: 7 residues within 4Å:- Chain G: H.63, C.67
- Chain H: P.53, D.54, H.59, R.62
- Ligands: ZN.38
4 PLIP interactions:3 interactions with chain H, 1 interactions with chain G- Water bridges: H:R.62
- Salt bridges: H:H.59, H:R.62, G:H.63
ACT.37: 7 residues within 4Å:- Chain B: P.53, D.54, H.59, R.62
- Chain H: H.63, C.67
- Ligands: ZN.11
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain H- Water bridges: B:R.62, H:H.63
- Salt bridges: B:H.59, B:R.62, H:H.63
ACT.43: 7 residues within 4Å:- Chain E: P.53, D.54, H.59, R.62
- Chain I: H.63, C.67
- Ligands: ZN.26
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain I- Water bridges: E:R.62
- Salt bridges: E:H.59, E:R.62, I:H.63
ACT.48: 7 residues within 4Å:- Chain C: P.53, D.54, H.59, R.62
- Chain J: H.63, C.67
- Ligands: ZN.52
4 PLIP interactions:1 interactions with chain J, 3 interactions with chain C- Salt bridges: J:H.63, C:H.59, C:R.62
- Water bridges: C:R.62
ACT.55: 7 residues within 4Å:- Chain K: H.63, C.67
- Chain L: P.53, D.54, H.59, R.62
- Ligands: ZN.58
4 PLIP interactions:3 interactions with chain L, 1 interactions with chain K- Water bridges: L:R.62
- Salt bridges: L:H.59, L:R.62, K:H.63
ACT.57: 7 residues within 4Å:- Chain F: P.53, D.54, H.59, R.62
- Chain L: H.63, C.67
- Ligands: ZN.31
5 PLIP interactions:3 interactions with chain F, 2 interactions with chain L- Water bridges: F:R.62, L:H.63
- Salt bridges: F:H.59, F:R.62, L:H.63
- 30 x ZN: ZINC ION(Non-covalent)
ZN.4: 3 residues within 4Å:- Chain A: A.1, D.39
- Chain E: H.77
5 PLIP interactions:1 interactions with chain E, 3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: E:H.77, A:A.1, A:D.39, A:D.39, H2O.2
ZN.5: 4 residues within 4Å:- Chain A: E.8, D.12
- Chain G: E.8, D.12
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain G- Metal complexes: A:E.8, A:D.12, G:E.8, G:D.12, G:D.12
ZN.6: 3 residues within 4Å:- Chain A: H.59
- Chain E: H.63
- Ligands: ACT.23
3 PLIP interactions:1 interactions with chain A, 1 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: A:H.59, E:H.63, H2O.20
ZN.9: 3 residues within 4Å:- Chain B: A.1, D.39
- Chain H: H.77
5 PLIP interactions:3 interactions with chain B, 1 interactions with chain H, 1 Ligand-Water interactions- Metal complexes: B:A.1, B:D.39, B:D.39, H:H.77, H2O.6
ZN.10: 4 residues within 4Å:- Chain B: E.8, D.12
- Chain D: E.8, D.12
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain D- Metal complexes: B:E.8, B:D.12, B:D.12, D:E.8, D:D.12
ZN.11: 4 residues within 4Å:- Chain B: D.54, H.59
- Chain H: H.63
- Ligands: ACT.37
3 PLIP interactions:1 interactions with chain B, 1 interactions with chain H, 1 Ligand-Water interactions- Metal complexes: B:H.59, H:H.63, H2O.7
ZN.12: 4 residues within 4Å:- Chain B: H.63
- Chain G: D.54, H.59
- Ligands: ACT.8
4 PLIP interactions:1 interactions with chain B, 2 interactions with chain G, 1 Ligand-Ligand interactions- Metal complexes: B:H.63, G:D.54, G:H.59, ACT.8
ZN.13: 3 residues within 4Å:- Chain B: H.77
- Chain G: A.1, D.39
4 PLIP interactions:1 interactions with chain B, 2 interactions with chain G, 1 Ligand-Water interactions- Metal complexes: B:H.77, G:A.1, G:D.39, H2O.27
ZN.18: 4 residues within 4Å:- Chain C: H.63
- Chain D: D.54, H.59
- Ligands: ACT.15
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Metal complexes: D:D.54, D:H.59, C:H.63
ZN.19: 3 residues within 4Å:- Chain C: H.77
- Chain D: A.1, D.39
5 PLIP interactions:1 interactions with chain C, 3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: C:H.77, D:A.1, D:D.39, D:D.39, H2O.14
ZN.24: 3 residues within 4Å:- Chain E: A.1, D.39
- Chain I: H.77
5 PLIP interactions:3 interactions with chain E, 1 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: E:A.1, E:D.39, E:D.39, I:H.77, H2O.18
ZN.25: 4 residues within 4Å:- Chain E: E.8, D.12
- Chain K: E.8, D.12
5 PLIP interactions:2 interactions with chain E, 3 interactions with chain K- Metal complexes: E:E.8, E:D.12, K:E.8, K:D.12, K:D.12
ZN.26: 3 residues within 4Å:- Chain E: H.59
- Chain I: H.63
- Ligands: ACT.43
3 PLIP interactions:1 interactions with chain E, 1 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: E:H.59, I:H.63, H2O.37
ZN.29: 3 residues within 4Å:- Chain F: A.1, D.39
- Chain L: H.77
5 PLIP interactions:3 interactions with chain F, 1 interactions with chain L, 1 Ligand-Water interactions- Metal complexes: F:A.1, F:D.39, F:D.39, L:H.77, H2O.23
ZN.30: 4 residues within 4Å:- Chain F: E.8, D.12
- Chain H: E.8, D.12
5 PLIP interactions:2 interactions with chain H, 3 interactions with chain F- Metal complexes: H:E.8, H:D.12, F:E.8, F:D.12, F:D.12
ZN.31: 4 residues within 4Å:- Chain F: D.54, H.59
- Chain L: H.63
- Ligands: ACT.57
3 PLIP interactions:1 interactions with chain F, 1 interactions with chain L, 1 Ligand-Water interactions- Metal complexes: F:H.59, L:H.63, H2O.24
ZN.32: 4 residues within 4Å:- Chain F: H.63
- Chain K: D.54, H.59
- Ligands: ACT.28
4 PLIP interactions:2 interactions with chain K, 1 interactions with chain F, 1 Ligand-Ligand interactions- Metal complexes: K:D.54, K:H.59, F:H.63, ACT.28
ZN.33: 3 residues within 4Å:- Chain F: H.77
- Chain K: A.1, D.39
4 PLIP interactions:1 interactions with chain F, 2 interactions with chain K, 1 Ligand-Water interactions- Metal complexes: F:H.77, K:A.1, K:D.39, H2O.43
ZN.38: 4 residues within 4Å:- Chain G: H.63
- Chain H: D.54, H.59
- Ligands: ACT.35
4 PLIP interactions:1 interactions with chain G, 2 interactions with chain H, 1 Ligand-Ligand interactions- Metal complexes: G:H.63, H:D.54, H:H.59, ACT.35
ZN.39: 3 residues within 4Å:- Chain G: H.77
- Chain H: A.1, D.39
5 PLIP interactions:1 interactions with chain G, 3 interactions with chain H, 1 Ligand-Water interactions- Metal complexes: G:H.77, H:A.1, H:D.39, H:D.39, H2O.31
ZN.44: 3 residues within 4Å:- Chain A: H.77
- Chain I: A.1, D.39
5 PLIP interactions:1 interactions with chain A, 3 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: A:H.77, I:A.1, I:D.39, I:D.39, H2O.35
ZN.45: 4 residues within 4Å:- Chain C: E.8, D.12
- Chain I: E.8, D.12
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain I- Metal complexes: C:E.8, C:D.12, C:D.12, I:E.8, I:D.12
ZN.46: 3 residues within 4Å:- Chain A: H.63
- Chain I: H.59
- Ligands: ACT.3
3 PLIP interactions:1 interactions with chain A, 1 interactions with chain I, 1 Ligand-Water interactions- Metal complexes: A:H.63, I:H.59, H2O.3
ZN.49: 3 residues within 4Å:- Chain D: H.77
- Chain J: A.1, D.39
5 PLIP interactions:1 interactions with chain D, 3 interactions with chain J, 1 Ligand-Water interactions- Metal complexes: D:H.77, J:A.1, J:D.39, J:D.39, H2O.40
ZN.50: 4 residues within 4Å:- Chain J: E.8, D.12
- Chain L: E.8, D.12
5 PLIP interactions:2 interactions with chain L, 3 interactions with chain J- Metal complexes: L:E.8, L:D.12, J:E.8, J:D.12, J:D.12
ZN.51: 4 residues within 4Å:- Chain D: H.63
- Chain J: D.54, H.59
- Ligands: ACT.17
3 PLIP interactions:1 interactions with chain D, 1 interactions with chain J, 1 Ligand-Water interactions- Metal complexes: D:H.63, J:H.59, H2O.41
ZN.52: 4 residues within 4Å:- Chain C: D.54, H.59
- Chain J: H.63
- Ligands: ACT.48
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain J- Metal complexes: C:D.54, C:H.59, J:H.63
ZN.53: 3 residues within 4Å:- Chain C: A.1, D.39
- Chain J: H.77
4 PLIP interactions:2 interactions with chain C, 1 interactions with chain J, 1 Ligand-Water interactions- Metal complexes: C:A.1, C:D.39, J:H.77, H2O.10
ZN.58: 4 residues within 4Å:- Chain K: H.63
- Chain L: D.54, H.59
- Ligands: ACT.55
4 PLIP interactions:2 interactions with chain L, 1 interactions with chain K, 1 Ligand-Ligand interactions- Metal complexes: L:D.54, L:H.59, K:H.63, ACT.55
ZN.59: 3 residues within 4Å:- Chain K: H.77
- Chain L: A.1, D.39
5 PLIP interactions:3 interactions with chain L, 1 interactions with chain K, 1 Ligand-Water interactions- Metal complexes: L:A.1, L:D.39, L:D.39, K:H.77, H2O.48
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ni, T.W. et al., Structural characterization of a microperoxidase inside a metal-directed protein cage. Angew.Chem.Int.Ed.Engl. (2010)
- Release Date
- 2011-01-12
- Peptides
- Soluble cytochrome b562: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-12-mer
- Ligands
- 3 x LYS- THR- THR- CYS- ASN- ALA- CYS- HIS- GLN: Heme-Peptide Fragment(Non-covalent)
- 15 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
- 12 x ACT: ACETATE ION(Non-functional Binders)
- 30 x ZN: ZINC ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ni, T.W. et al., Structural characterization of a microperoxidase inside a metal-directed protein cage. Angew.Chem.Int.Ed.Engl. (2010)
- Release Date
- 2011-01-12
- Peptides
- Soluble cytochrome b562: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
D