- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-24-mer
- Ligands
- 24 x ZN: ZINC ION(Non-covalent)
- 12 x ZNH: PROTOPORPHYRIN IX CONTAINING ZN(Non-covalent)
ZNH.2: 18 residues within 4Å:- Chain A: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59
- Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53
18 PLIP interactions:7 interactions with chain B, 11 interactions with chain A,- Hydrophobic interactions: B:L.19, B:F.26, B:F.26, B:I.49, B:M.52, A:L.19, A:I.22, A:I.22, A:F.26, A:F.26, A:I.49, A:I.49, A:M.52, A:A.55, A:I.59
- Water bridges: B:Y.45
- Salt bridges: B:K.53, A:K.53
ZNH.13: 16 residues within 4Å:- Chain C: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, I.59
- Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55
17 PLIP interactions:9 interactions with chain D, 8 interactions with chain C,- Hydrophobic interactions: D:L.19, D:F.26, D:M.52, D:A.55, C:L.19, C:I.22, C:I.22, C:F.26, C:F.26, C:M.52, C:I.59
- Water bridges: D:Y.45, D:Y.45, D:K.53, D:K.53
- Salt bridges: D:K.53, C:K.53
ZNH.21: 16 residues within 4Å:- Chain E: L.19, N.23, F.26, Y.45, M.52, K.53
- Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59, L.71
15 PLIP interactions:5 interactions with chain E, 10 interactions with chain F,- Hydrophobic interactions: E:L.19, E:F.26, E:Y.45, E:M.52, F:L.19, F:I.22, F:I.22, F:F.26, F:F.26, F:I.49, F:M.52, F:I.59, F:L.71
- Salt bridges: E:K.53, F:K.53
ZNH.29: 17 residues within 4Å:- Chain G: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59
- Chain H: L.19, I.22, N.23, F.26, Y.45, M.52, K.53, A.55
13 PLIP interactions:8 interactions with chain G, 5 interactions with chain H,- Hydrophobic interactions: G:L.19, G:I.22, G:I.22, G:F.26, G:F.26, G:M.52, G:I.59, H:L.19, H:F.26, H:M.52, H:A.55
- Salt bridges: G:K.53, H:K.53
ZNH.39: 17 residues within 4Å:- Chain I: L.19, N.23, F.26, Y.45, I.49, M.52, K.53, A.55
- Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59
16 PLIP interactions:10 interactions with chain J, 6 interactions with chain I,- Hydrophobic interactions: J:L.19, J:I.22, J:I.22, J:F.26, J:F.26, J:I.49, J:M.52, J:I.59, I:L.19, I:F.26, I:Y.45, I:M.52, I:A.55
- Water bridges: J:K.53
- Salt bridges: J:K.53, I:K.53
ZNH.44: 19 residues within 4Å:- Chain K: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59
- Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55
17 PLIP interactions:11 interactions with chain K, 6 interactions with chain L,- Hydrophobic interactions: K:L.19, K:I.22, K:I.22, K:F.26, K:F.26, K:I.49, K:M.52, K:A.55, K:I.59, L:L.19, L:F.26, L:F.26, L:M.52, L:A.55
- Water bridges: K:Y.45
- Salt bridges: K:K.53, L:K.53
ZNH.52: 18 residues within 4Å:- Chain M: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59
- Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53
19 PLIP interactions:8 interactions with chain N, 11 interactions with chain M,- Hydrophobic interactions: N:L.19, N:F.26, N:F.26, N:I.49, N:M.52, M:L.19, M:I.22, M:I.22, M:F.26, M:F.26, M:I.49, M:I.49, M:M.52, M:A.55, M:I.59
- Water bridges: N:Y.45, N:Y.45
- Salt bridges: N:K.53, M:K.53
ZNH.63: 16 residues within 4Å:- Chain O: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, I.59
- Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55
16 PLIP interactions:8 interactions with chain O, 8 interactions with chain P,- Hydrophobic interactions: O:L.19, O:I.22, O:I.22, O:F.26, O:F.26, O:M.52, O:I.59, P:L.19, P:F.26, P:M.52, P:A.55
- Salt bridges: O:K.53, P:K.53
- Water bridges: P:Y.45, P:K.53, P:K.53
ZNH.71: 16 residues within 4Å:- Chain Q: L.19, N.23, F.26, Y.45, M.52, K.53
- Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59, L.71
15 PLIP interactions:10 interactions with chain R, 5 interactions with chain Q,- Hydrophobic interactions: R:L.19, R:I.22, R:I.22, R:F.26, R:F.26, R:I.49, R:M.52, R:I.59, R:L.71, Q:L.19, Q:F.26, Q:Y.45, Q:M.52
- Salt bridges: R:K.53, Q:K.53
ZNH.79: 17 residues within 4Å:- Chain S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59
- Chain T: L.19, I.22, N.23, F.26, Y.45, M.52, K.53, A.55
13 PLIP interactions:8 interactions with chain S, 5 interactions with chain T,- Hydrophobic interactions: S:L.19, S:I.22, S:I.22, S:F.26, S:F.26, S:M.52, S:I.59, T:L.19, T:F.26, T:M.52, T:A.55
- Salt bridges: S:K.53, T:K.53
ZNH.89: 17 residues within 4Å:- Chain U: L.19, N.23, F.26, Y.45, I.49, M.52, K.53, A.55
- Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59
16 PLIP interactions:10 interactions with chain V, 6 interactions with chain U,- Hydrophobic interactions: V:L.19, V:I.22, V:I.22, V:F.26, V:F.26, V:I.49, V:M.52, V:I.59, U:L.19, U:F.26, U:Y.45, U:M.52, U:A.55
- Water bridges: V:K.53
- Salt bridges: V:K.53, U:K.53
ZNH.94: 19 residues within 4Å:- Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59
- Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55
18 PLIP interactions:12 interactions with chain W, 6 interactions with chain X,- Hydrophobic interactions: W:L.19, W:I.22, W:I.22, W:F.26, W:F.26, W:I.49, W:M.52, W:A.55, W:I.59, X:L.19, X:F.26, X:F.26, X:M.52, X:A.55
- Water bridges: W:Y.45, W:Y.45
- Salt bridges: W:K.53, X:K.53
- 8 x NA: SODIUM ION(Non-functional Binders)
NA.3: 5 residues within 4Å:- Chain A: N.148
- Chain C: N.148
- Chain M: N.148
- Chain O: N.148
- Ligands: NA.53
5 PLIP interactions:2 interactions with chain A, 1 interactions with chain O, 1 interactions with chain C, 1 interactions with chain M- Hydrogen bonds: A:N.148, A:N.148, O:N.148, C:N.148, M:N.148
NA.8: 4 residues within 4Å:- Chain B: N.148
- Chain G: N.148
- Chain J: N.148
- Chain K: N.148
5 PLIP interactions:1 interactions with chain G, 1 interactions with chain K, 2 interactions with chain J, 1 interactions with chain B- Hydrogen bonds: G:N.148, K:N.148, J:N.148, J:N.148, B:N.148
NA.17: 4 residues within 4Å:- Chain D: N.148
- Chain H: N.148
- Chain Q: N.148
- Chain U: N.148
5 PLIP interactions:1 interactions with chain U, 1 interactions with chain Q, 2 interactions with chain D, 1 interactions with chain H- Hydrogen bonds: U:N.148, Q:N.148, D:N.148, D:N.148, H:N.148
NA.25: 5 residues within 4Å:- Chain F: N.148
- Chain L: N.148
- Chain R: N.148
- Chain X: N.148
- Ligands: NA.75
5 PLIP interactions:1 interactions with chain X, 2 interactions with chain F, 1 interactions with chain R, 1 interactions with chain L- Hydrogen bonds: X:N.148, F:N.148, F:N.148, R:N.148, L:N.148
NA.53: 5 residues within 4Å:- Chain A: N.148
- Chain C: N.148
- Chain M: N.148
- Chain O: N.148
- Ligands: NA.3
5 PLIP interactions:1 interactions with chain O, 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain M- Hydrogen bonds: O:N.148, C:N.148, A:N.148, A:N.148, M:N.148
NA.58: 4 residues within 4Å:- Chain N: N.148
- Chain S: N.148
- Chain V: N.148
- Chain W: N.148
5 PLIP interactions:1 interactions with chain N, 1 interactions with chain S, 1 interactions with chain V, 2 interactions with chain W- Hydrogen bonds: N:N.148, S:N.148, V:N.148, W:N.148, W:N.148
NA.67: 4 residues within 4Å:- Chain E: N.148
- Chain I: N.148
- Chain P: N.148
- Chain T: N.148
5 PLIP interactions:2 interactions with chain E, 1 interactions with chain P, 1 interactions with chain T, 1 interactions with chain I- Hydrogen bonds: E:N.148, E:N.148, P:N.148, T:N.148, I:N.148
NA.75: 5 residues within 4Å:- Chain F: N.148
- Chain L: N.148
- Chain R: N.148
- Chain X: N.148
- Ligands: NA.25
5 PLIP interactions:1 interactions with chain L, 2 interactions with chain F, 1 interactions with chain R, 1 interactions with chain X- Hydrogen bonds: L:N.148, F:N.148, F:N.148, R:N.148, X:N.148
- 56 x MLI: MALONATE ION(Non-functional Binders)
MLI.4: 4 residues within 4Å:- Chain A: R.57, V.115, M.119
- Chain J: R.125
Ligand excluded by PLIPMLI.5: 8 residues within 4Å:- Chain A: R.117, D.118, I.121
- Chain J: R.117, I.121
- Chain P: R.117, D.118, I.121
Ligand excluded by PLIPMLI.6: 3 residues within 4Å:- Chain A: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.9: 3 residues within 4Å:- Chain B: R.57, M.119
- Chain C: R.125
Ligand excluded by PLIPMLI.10: 7 residues within 4Å:- Chain B: R.117, D.118, I.121
- Chain C: R.117, I.121
- Chain H: R.117, I.121
Ligand excluded by PLIPMLI.11: 3 residues within 4Å:- Chain B: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.14: 4 residues within 4Å:- Chain C: R.57, V.115, M.119
- Chain H: R.125
Ligand excluded by PLIPMLI.15: 3 residues within 4Å:- Chain C: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.18: 3 residues within 4Å:- Chain D: R.57, M.119
- Chain M: R.125
Ligand excluded by PLIPMLI.19: 3 residues within 4Å:- Chain D: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.22: 4 residues within 4Å:- Chain E: R.57, V.115, M.119
- Chain X: R.125
Ligand excluded by PLIPMLI.23: 3 residues within 4Å:- Chain E: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.26: 3 residues within 4Å:- Chain F: R.57, M.119
- Chain I: R.125
Ligand excluded by PLIPMLI.27: 3 residues within 4Å:- Chain F: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.30: 5 residues within 4Å:- Chain G: R.57, R.61, V.115, M.119
- Chain Q: R.125
Ligand excluded by PLIPMLI.31: 3 residues within 4Å:- Chain G: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.33: 3 residues within 4Å:- Chain B: R.125
- Chain H: R.57, M.119
Ligand excluded by PLIPMLI.34: 3 residues within 4Å:- Chain H: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.36: 3 residues within 4Å:- Chain I: R.57, M.119
- Chain K: R.125
Ligand excluded by PLIPMLI.37: 3 residues within 4Å:- Chain I: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.38: 8 residues within 4Å:- Chain F: R.117, I.121
- Chain I: R.117, D.118, I.121
- Chain K: R.117, D.118, I.121
Ligand excluded by PLIPMLI.41: 3 residues within 4Å:- Chain J: R.57, M.119
- Chain P: R.125
Ligand excluded by PLIPMLI.42: 3 residues within 4Å:- Chain J: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.45: 3 residues within 4Å:- Chain F: R.125
- Chain K: R.57, M.119
Ligand excluded by PLIPMLI.46: 3 residues within 4Å:- Chain K: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.48: 3 residues within 4Å:- Chain G: R.125
- Chain L: R.57, M.119
Ligand excluded by PLIPMLI.49: 8 residues within 4Å:- Chain G: R.117, D.118, I.121
- Chain L: R.117, D.118, I.121
- Chain Q: R.117, I.121
Ligand excluded by PLIPMLI.50: 3 residues within 4Å:- Chain L: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.54: 4 residues within 4Å:- Chain M: R.57, V.115, M.119
- Chain V: R.125
Ligand excluded by PLIPMLI.55: 8 residues within 4Å:- Chain D: R.117, D.118, I.121
- Chain M: R.117, D.118, I.121
- Chain V: R.117, I.121
Ligand excluded by PLIPMLI.56: 3 residues within 4Å:- Chain M: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.59: 3 residues within 4Å:- Chain N: R.57, M.119
- Chain O: R.125
Ligand excluded by PLIPMLI.60: 7 residues within 4Å:- Chain N: R.117, D.118, I.121
- Chain O: R.117, I.121
- Chain T: R.117, I.121
Ligand excluded by PLIPMLI.61: 3 residues within 4Å:- Chain N: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.64: 4 residues within 4Å:- Chain O: R.57, V.115, M.119
- Chain T: R.125
Ligand excluded by PLIPMLI.65: 3 residues within 4Å:- Chain O: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.68: 3 residues within 4Å:- Chain A: R.125
- Chain P: R.57, M.119
Ligand excluded by PLIPMLI.69: 3 residues within 4Å:- Chain P: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.72: 4 residues within 4Å:- Chain L: R.125
- Chain Q: R.57, V.115, M.119
Ligand excluded by PLIPMLI.73: 3 residues within 4Å:- Chain Q: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.76: 3 residues within 4Å:- Chain R: R.57, M.119
- Chain U: R.125
Ligand excluded by PLIPMLI.77: 3 residues within 4Å:- Chain R: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.80: 5 residues within 4Å:- Chain E: R.125
- Chain S: R.57, R.61, V.115, M.119
Ligand excluded by PLIPMLI.81: 3 residues within 4Å:- Chain S: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.83: 3 residues within 4Å:- Chain N: R.125
- Chain T: R.57, M.119
Ligand excluded by PLIPMLI.84: 3 residues within 4Å:- Chain T: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.86: 3 residues within 4Å:- Chain U: R.57, M.119
- Chain W: R.125
Ligand excluded by PLIPMLI.87: 3 residues within 4Å:- Chain U: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.88: 8 residues within 4Å:- Chain R: R.117, I.121
- Chain U: R.117, D.118, I.121
- Chain W: R.117, D.118, I.121
Ligand excluded by PLIPMLI.91: 3 residues within 4Å:- Chain D: R.125
- Chain V: R.57, M.119
Ligand excluded by PLIPMLI.92: 3 residues within 4Å:- Chain V: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.95: 3 residues within 4Å:- Chain R: R.125
- Chain W: R.57, M.119
Ligand excluded by PLIPMLI.96: 3 residues within 4Å:- Chain W: G.145, L.146, Q.147
Ligand excluded by PLIPMLI.98: 3 residues within 4Å:- Chain S: R.125
- Chain X: R.57, M.119
Ligand excluded by PLIPMLI.99: 8 residues within 4Å:- Chain E: R.117, I.121
- Chain S: R.117, D.118, I.121
- Chain X: R.117, D.118, I.121
Ligand excluded by PLIPMLI.100: 3 residues within 4Å:- Chain X: G.145, L.146, Q.147
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Benavides, B.S. et al., Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction. Biochemistry (2020)
- Release Date
- 2020-05-13
- Peptides
- Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
AN
BO
CP
DQ
ER
FS
GT
HU
IV
JW
KX
L
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-24-mer
- Ligands
- 24 x ZN: ZINC ION(Non-covalent)
- 12 x ZNH: PROTOPORPHYRIN IX CONTAINING ZN(Non-covalent)
- 8 x NA: SODIUM ION(Non-functional Binders)
- 56 x MLI: MALONATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Benavides, B.S. et al., Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction. Biochemistry (2020)
- Release Date
- 2020-05-13
- Peptides
- Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
AN
BO
CP
DQ
ER
FS
GT
HU
IV
JW
KX
L