SMTL ID : 3m4b.1

A Zn-mediated tetrahedral protein lattice cage

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-12-mer

Ligands

12 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 18 residues within 4Å: Chain A: L.3, 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 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:L.3, 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 Metal complexes: A:H.102 HEM.7: 19 residues within 4Å: Chain B: L.3, 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 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.3, B:M.7, B:L.10, B:L.10, B:N.11, B:L.14, B:P.45, B:F.65, B:F.65, B:L.68, B:R.106 Hydrogen bonds: B:E.4 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEM.14: 16 residues within 4Å: Chain C: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:L.14, C:P.45, C:F.61, C:F.61, 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: 19 residues within 4Å: Chain D: L.3, 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 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:L.10, D:N.11, D:L.14, D:P.45, D:F.65, D:F.65, D:L.68, D:R.106 pi-Stacking: D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102 HEM.21: 18 residues within 4Å: Chain E: L.3, 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 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:L.3, 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 Metal complexes: E:H.102 HEM.27: 19 residues within 4Å: Chain F: L.3, 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 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:L.3, F:M.7, F:L.10, F:L.10, F:N.11, F:L.14, F:P.45, F:F.65, F:F.65, F:L.68, F:R.106 Hydrogen bonds: F:E.4 pi-Cation interactions: F:R.106 Metal complexes: F:H.102 HEM.34: 16 residues within 4Å: Chain G: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain G, Hydrophobic interactions: G:M.7, G:L.10, G:L.14, G:P.45, G:F.61, G:F.65, G:F.65, G:L.68, G:R.106 pi-Stacking: G:H.102, G:H.102 Metal complexes: G:H.102 HEM.36: 19 residues within 4Å: Chain H: L.3, 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 13 PLIP interactions: 13 interactions with chain H, Hydrophobic interactions: H:L.3, H:M.7, H:L.10, H:N.11, H:L.14, H:P.45, H:F.65, H:F.65, H:L.68, H:R.106 pi-Stacking: H:H.102 pi-Cation interactions: H:R.106 Metal complexes: H:H.102 HEM.41: 18 residues within 4Å: Chain I: L.3, 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 13 PLIP interactions: 13 interactions with chain I, Hydrophobic interactions: I:L.3, 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 Metal complexes: I:H.102 HEM.47: 19 residues within 4Å: Chain J: L.3, 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 14 PLIP interactions: 14 interactions with chain J, Hydrophobic interactions: J:L.3, J:M.7, J:L.10, J:L.10, J:N.11, J:L.14, J:P.45, J:F.65, J:F.65, J:L.68, J:R.106 Hydrogen bonds: J:E.4 pi-Cation interactions: J:R.106 Metal complexes: J:H.102 HEM.54: 16 residues within 4Å: Chain K: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain K, Hydrophobic interactions: K:M.7, K:L.10, K:L.14, K:P.45, K:F.61, K:F.65, K:F.65, K:L.68, K:R.106 pi-Stacking: K:H.102, K:H.102 Metal complexes: K:H.102 HEM.56: 19 residues within 4Å: Chain L: L.3, 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 13 PLIP interactions: 13 interactions with chain L, Hydrophobic interactions: L:L.3, L:M.7, L:L.10, L:N.11, L:L.14, L:P.45, L:F.65, L:F.65, L:L.68, L:R.106 pi-Stacking: L:H.102 pi-Cation interactions: L:R.106 Metal complexes: L:H.102

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: H.63, C.67 Chain I: P.53, D.54, H.59, R.62 Ligands: ZN.45 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain A Salt bridges: I:H.59, I:R.62, A:H.63 ACT.8: 5 residues within 4Å: Chain B: C.67 Chain G: P.53, H.59, R.62 Ligands: ZN.12 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:H.59 ACT.15: 8 residues within 4Å: Chain C: H.63, W.66, C.67 Chain D: P.53, D.54, H.59, R.62 Ligands: ZN.18 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Salt bridges: C:H.63, D:H.59, D:R.62 Hydrophobic interactions: D:P.53 ACT.17: 9 residues within 4Å: Chain D: H.63, C.67, Q.71, T.97 Chain J: P.53, D.54, H.59, R.62 Ligands: ZN.51 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain D Salt bridges: J:H.59, J:R.62, D:H.63 Hydrophobic interactions: D:T.97 ACT.22: 7 residues within 4Å: Chain A: P.53, D.54, H.59, R.62 Chain E: H.63, C.67 Ligands: ZN.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Salt bridges: A:H.59, A:R.62, E:H.63 ACT.28: 5 residues within 4Å: Chain F: C.67 Chain K: P.53, H.59, R.62 Ligands: ZN.32 1 PLIP interactions: 1 interactions with chain K Salt bridges: K:H.59 ACT.35: 8 residues within 4Å: Chain G: H.63, W.66, 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 Hydrophobic interactions: H:P.53 Salt bridges: H:H.59, H:R.62, G:H.63 ACT.37: 9 residues within 4Å: Chain B: P.53, D.54, H.59, R.62 Chain H: H.63, C.67, Q.71, T.97 Ligands: ZN.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain H Salt bridges: B:H.59, B:R.62, H:H.63 Hydrophobic interactions: H:T.97 ACT.42: 7 residues within 4Å: Chain E: P.53, D.54, H.59, R.62 Chain I: H.63, C.67 Ligands: ZN.25 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain E Salt bridges: I:H.63, E:H.59, E:R.62 ACT.48: 5 residues within 4Å: Chain C: P.53, H.59, R.62 Chain J: C.67 Ligands: ZN.52 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.59 ACT.55: 8 residues within 4Å: Chain K: H.63, W.66, 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 Hydrophobic interactions: L:P.53 Salt bridges: L:H.59, L:R.62, K:H.63 ACT.57: 9 residues within 4Å: Chain F: P.53, D.54, H.59, R.62 Chain L: H.63, C.67, Q.71, T.97 Ligands: ZN.31 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain F Hydrophobic interactions: L:T.97 Salt bridges: L:H.63, F:H.59, F:R.62

36 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: A.1, D.39 Chain E: H.77 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:A.1, A:D.39, A:D.39, E:H.77, H2O.1 ZN.4: 4 residues within 4Å: Chain A: E.8, D.12 Chain G: E.8, D.12 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain A Metal complexes: G:E.8, G:D.12, G:D.12, A:E.8, A:D.12 ZN.5: 3 residues within 4Å: Chain A: H.59 Chain E: H.63 Ligands: ACT.22 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:H.63, A:H.59, H2O.1 ZN.6: 2 residues within 4Å: Chain A: K.51, E.57 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.57, H2O.1 ZN.9: 3 residues within 4Å: Chain B: A.1, D.39 Chain H: H.77 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: H:H.77, B:A.1, B:D.39, B:D.39, H2O.2 ZN.10: 4 residues within 4Å: Chain B: E.8, D.12 Chain D: E.8, D.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Metal complexes: B:E.8, B:D.12, D:E.8, D:D.12, 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.2 ZN.12: 2 residues within 4Å: Chain G: H.59 Ligands: ACT.8 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.59 ZN.13: 3 residues within 4Å: Chain B: H.77 Chain G: A.1, D.39 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain B Metal complexes: G:A.1, G:D.39, B:H.77 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 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:A.1, D:D.39, C:H.77 ZN.20: 1 residues within 4Å: Chain D: E.4 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.4 ZN.23: 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.4 ZN.24: 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.25: 3 residues within 4Å: Chain E: H.59 Chain I: H.63 Ligands: ACT.42 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: I:H.63, E:H.59, H2O.4 ZN.26: 2 residues within 4Å: Chain E: K.51, E.57 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.57, H2O.4 ZN.29: 3 residues within 4Å: Chain F: A.1, D.39 Chain L: H.77 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: L:H.77, F:A.1, F:D.39, F:D.39, H2O.5 ZN.30: 4 residues within 4Å: Chain F: E.8, D.12 Chain H: E.8, D.12 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain F Metal complexes: H:E.8, H:D.12, H:D.12, F:E.8, 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 L, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: L:H.63, F:H.59, H2O.5 ZN.32: 2 residues within 4Å: Chain K: H.59 Ligands: ACT.28 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:H.59 ZN.33: 3 residues within 4Å: Chain F: H.77 Chain K: A.1, D.39 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain F Metal complexes: K:A.1, K:D.39, F:H.77 ZN.38: 4 residues within 4Å: Chain G: H.63 Chain H: D.54, H.59 Ligands: ACT.35 4 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: H:D.54, H:H.59, G:H.63, ACT.35 ZN.39: 3 residues within 4Å: Chain G: H.77 Chain H: A.1, D.39 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G Metal complexes: H:A.1, H:D.39, G:H.77 ZN.40: 1 residues within 4Å: Chain H: E.4 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.4 ZN.43: 3 residues within 4Å: Chain A: H.77 Chain I: A.1, D.39 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: I:A.1, I:D.39, I:D.39, A:H.77, H2O.7 ZN.44: 4 residues within 4Å: Chain C: E.8, D.12 Chain I: E.8, D.12 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain C Metal complexes: I:E.8, I:D.12, C:E.8, C:D.12, C:D.12 ZN.45: 3 residues within 4Å: Chain A: H.63 Chain I: H.59 Ligands: ACT.2 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.7 ZN.46: 2 residues within 4Å: Chain I: K.51, E.57 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.57, H2O.8 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.8 ZN.50: 4 residues within 4Å: Chain J: E.8, D.12 Chain L: E.8, D.12 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain J Metal complexes: L:E.8, L:D.12, L:D.12, J:E.8, 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.8 ZN.52: 2 residues within 4Å: Chain C: H.59 Ligands: ACT.48 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.59 ZN.53: 3 residues within 4Å: Chain C: A.1, D.39 Chain J: H.77 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain C Metal complexes: J:H.77, C:A.1, C:D.39 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 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K Metal complexes: L:A.1, L:D.39, K:H.77 ZN.60: 1 residues within 4Å: Chain L: E.4 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.4

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
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Soluble cytochrome b562

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