- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-16-mer
- Ligands
- 32 x FE: FE (III) ION(Non-covalent)
- 51 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 5 residues within 4Å:- Chain A: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.4: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPSO4.5: 3 residues within 4Å:- Chain A: P.161, S.162, S.163
Ligand excluded by PLIPSO4.6: 4 residues within 4Å:- Chain A: T.75, T.76, Q.77
- Ligands: SO4.9
Ligand excluded by PLIPSO4.7: 6 residues within 4Å:- Chain A: K.78, G.80, K.81, V.82
- Chain B: T.76, Q.77
Ligand excluded by PLIPSO4.9: 7 residues within 4Å:- Chain A: T.76, Q.77
- Chain B: K.78, K.81, V.82
- Ligands: SO4.6, GOL.16
Ligand excluded by PLIPSO4.12: 5 residues within 4Å:- Chain B: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.13: 3 residues within 4Å:- Chain B: K.114
- Chain G: K.114
- Chain N: K.114
Ligand excluded by PLIPSO4.14: 3 residues within 4Å:- Chain B: P.161, S.162, S.163
Ligand excluded by PLIPSO4.20: 5 residues within 4Å:- Chain C: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.21: 3 residues within 4Å:- Chain C: S.144, K.147, N.148
Ligand excluded by PLIPSO4.22: 3 residues within 4Å:- Chain C: P.161, S.162, S.163
Ligand excluded by PLIPSO4.26: 6 residues within 4Å:- Chain D: K.50, S.162, S.163, T.164, G.165
- Ligands: FEC.29
Ligand excluded by PLIPSO4.27: 3 residues within 4Å:- Chain D: S.144, K.147, N.148
Ligand excluded by PLIPSO4.31: 2 residues within 4Å:- Chain D: K.114
- Chain E: K.114
Ligand excluded by PLIPSO4.34: 5 residues within 4Å:- Chain E: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.35: 3 residues within 4Å:- Chain E: P.161, S.162, S.163
Ligand excluded by PLIPSO4.40: 5 residues within 4Å:- Chain F: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.41: 2 residues within 4Å:- Chain F: N.4, R.5
Ligand excluded by PLIPSO4.42: 3 residues within 4Å:- Chain F: P.161, S.162, S.163
Ligand excluded by PLIPSO4.48: 2 residues within 4Å:- Chain G: S.144, N.148
Ligand excluded by PLIPSO4.49: 3 residues within 4Å:- Chain G: P.161, S.162, S.163
Ligand excluded by PLIPSO4.50: 5 residues within 4Å:- Chain G: L.149, G.150, D.151, T.152
- Chain M: D.151
Ligand excluded by PLIPSO4.56: 5 residues within 4Å:- Chain H: K.50, S.163, T.164, G.165
- Ligands: FEC.51
Ligand excluded by PLIPSO4.57: 2 residues within 4Å:- Chain H: S.144, N.148
Ligand excluded by PLIPSO4.58: 3 residues within 4Å:- Chain H: P.161, S.162, S.163
Ligand excluded by PLIPSO4.63: 5 residues within 4Å:- Chain I: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.64: 1 residues within 4Å:- Chain I: R.5
Ligand excluded by PLIPSO4.65: 3 residues within 4Å:- Chain I: S.144, K.147, N.148
Ligand excluded by PLIPSO4.66: 3 residues within 4Å:- Chain I: P.161, S.162, S.163
Ligand excluded by PLIPSO4.72: 6 residues within 4Å:- Chain J: K.50, S.162, S.163, T.164, G.165
- Ligands: FEC.67
Ligand excluded by PLIPSO4.73: 1 residues within 4Å:- Chain J: K.114
Ligand excluded by PLIPSO4.74: 4 residues within 4Å:- Chain J: T.160, P.161, S.162, S.163
Ligand excluded by PLIPSO4.77: 3 residues within 4Å:- Chain F: K.114
- Chain K: K.114
- Chain P: K.114
Ligand excluded by PLIPSO4.80: 5 residues within 4Å:- Chain K: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.81: 3 residues within 4Å:- Chain K: S.144, K.147, N.148
Ligand excluded by PLIPSO4.82: 3 residues within 4Å:- Chain K: P.161, S.162, S.163
Ligand excluded by PLIPSO4.86: 6 residues within 4Å:- Chain L: K.50, S.162, S.163, T.164, G.165
- Ligands: FEC.90
Ligand excluded by PLIPSO4.87: 2 residues within 4Å:- Chain L: N.4, R.5
Ligand excluded by PLIPSO4.88: 3 residues within 4Å:- Chain L: S.144, K.147, N.148
Ligand excluded by PLIPSO4.89: 3 residues within 4Å:- Chain L: G.150, D.151, T.152
Ligand excluded by PLIPSO4.93: 5 residues within 4Å:- Chain M: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.94: 3 residues within 4Å:- Chain M: P.161, S.162, S.163
Ligand excluded by PLIPSO4.100: 5 residues within 4Å:- Chain N: K.50, S.162, S.163, T.164, G.165
Ligand excluded by PLIPSO4.101: 3 residues within 4Å:- Chain N: S.144, K.147, N.148
Ligand excluded by PLIPSO4.102: 3 residues within 4Å:- Chain N: P.161, S.162, S.163
Ligand excluded by PLIPSO4.106: 3 residues within 4Å:- Chain O: P.161, S.162, S.163
Ligand excluded by PLIPSO4.107: 2 residues within 4Å:- Chain O: R.123, R.127
Ligand excluded by PLIPSO4.112: 6 residues within 4Å:- Chain P: K.50, S.162, S.163, T.164, G.165
- Ligands: FEC.115
Ligand excluded by PLIPSO4.113: 2 residues within 4Å:- Chain P: S.144, N.148
Ligand excluded by PLIPSO4.114: 3 residues within 4Å:- Chain P: P.161, S.162, S.163
Ligand excluded by PLIP- 24 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 6 residues within 4Å:- Chain A: R.58, H.59, N.62, L.124, R.127, E.131
Ligand excluded by PLIPGOL.16: 5 residues within 4Å:- Chain A: Q.77, K.78
- Chain B: Q.77, K.78
- Ligands: SO4.9
Ligand excluded by PLIPGOL.17: 7 residues within 4Å:- Chain B: R.58, H.59, N.62, L.124, R.127, I.128, E.131
Ligand excluded by PLIPGOL.23: 7 residues within 4Å:- Chain C: R.58, H.59, N.62, L.124, R.127, I.128, E.131
Ligand excluded by PLIPGOL.30: 4 residues within 4Å:- Chain C: Q.77, K.78
- Chain D: Q.77, K.78
Ligand excluded by PLIPGOL.36: 7 residues within 4Å:- Chain E: R.58, H.59, N.62, L.124, R.127, I.128, E.131
Ligand excluded by PLIPGOL.37: 4 residues within 4Å:- Chain E: Q.77, K.78
- Chain F: Q.77, K.78
Ligand excluded by PLIPGOL.44: 5 residues within 4Å:- Chain F: R.58, H.59, N.62, R.127, E.131
Ligand excluded by PLIPGOL.45: 3 residues within 4Å:- Chain F: P.89, V.90, K.147
Ligand excluded by PLIPGOL.52: 5 residues within 4Å:- Chain G: R.58, H.59, N.62, R.127, E.131
Ligand excluded by PLIPGOL.53: 4 residues within 4Å:- Chain G: Q.77, K.78
- Chain H: Q.77, K.78
Ligand excluded by PLIPGOL.59: 7 residues within 4Å:- Chain H: R.58, H.59, N.62, L.124, R.127, I.128, E.131
Ligand excluded by PLIPGOL.60: 6 residues within 4Å:- Chain H: R.5, K.9, G.117
- Chain I: D.100, I.103, E.104
Ligand excluded by PLIPGOL.68: 5 residues within 4Å:- Chain H: R.123, R.127
- Chain I: R.123, R.127
- Ligands: GOL.69
Ligand excluded by PLIPGOL.69: 8 residues within 4Å:- Chain I: R.58, H.59, N.62, L.124, R.127, I.128, E.131
- Ligands: GOL.68
Ligand excluded by PLIPGOL.75: 4 residues within 4Å:- Chain I: Q.77, K.78
- Chain J: Q.77, K.78
Ligand excluded by PLIPGOL.76: 6 residues within 4Å:- Chain J: H.59, N.62, L.124, R.127, I.128, E.131
Ligand excluded by PLIPGOL.83: 4 residues within 4Å:- Chain K: Q.77, K.78
- Chain L: Q.77, K.78
Ligand excluded by PLIPGOL.96: 5 residues within 4Å:- Chain M: R.58, N.62, L.124, R.127, E.131
Ligand excluded by PLIPGOL.97: 4 residues within 4Å:- Chain M: Q.77, K.78
- Chain N: Q.77, K.78
Ligand excluded by PLIPGOL.103: 5 residues within 4Å:- Chain N: H.59, N.62, L.124, R.127, E.131
Ligand excluded by PLIPGOL.108: 5 residues within 4Å:- Chain O: R.58, H.59, N.62, R.127, E.131
Ligand excluded by PLIPGOL.109: 4 residues within 4Å:- Chain O: Q.77, K.78
- Chain P: Q.77, K.78
Ligand excluded by PLIPGOL.116: 6 residues within 4Å:- Chain P: R.58, H.59, N.62, L.124, R.127, E.131
Ligand excluded by PLIP- 8 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Covalent)(Non-covalent)
FEC.15: 23 residues within 4Å:- Chain A: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169
- Chain B: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
22 PLIP interactions:11 interactions with chain A, 11 interactions with chain B,- Hydrophobic interactions: A:L.24, A:I.27, A:M.31, A:I.54, A:E.61, B:I.27, B:M.31, B:M.57, B:E.61
- Hydrogen bonds: A:Y.35, A:Y.35, B:Y.35, B:S.168, B:S.168, B:K.169
- Salt bridges: A:R.20, A:H.28, A:K.169, A:K.169, B:R.20, B:K.50
- Water bridges: B:R.20
FEC.29: 24 residues within 4Å:- Chain C: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169
- Chain D: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
- Ligands: SO4.26
21 PLIP interactions:12 interactions with chain D, 9 interactions with chain C,- Hydrophobic interactions: D:I.27, D:M.31, D:M.57, D:E.61, C:L.24, C:I.27, C:M.31, C:E.61
- Hydrogen bonds: D:S.168, D:S.168, D:S.168, D:K.169, C:Y.35
- Water bridges: D:R.20, C:R.20
- Salt bridges: D:R.20, D:K.50, D:K.169, C:R.20, C:K.169, C:K.169
FEC.43: 22 residues within 4Å:- Chain E: R.20, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169
- Chain F: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
21 PLIP interactions:9 interactions with chain E, 12 interactions with chain F,- Hydrophobic interactions: E:I.27, E:I.27, E:M.31, E:I.54, E:E.61, F:I.27, F:M.31, F:M.57, F:E.61
- Hydrogen bonds: E:Y.35, F:S.168, F:S.168, F:K.169
- Salt bridges: E:R.20, E:K.169, E:K.169, F:R.20, F:K.50
- Water bridges: F:R.20, F:N.32, F:T.164
FEC.51: 24 residues within 4Å:- Chain G: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, M.57, A.60, E.61, S.168, K.169
- Chain H: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, R.58, E.61, S.168, K.169
- Ligands: SO4.56
21 PLIP interactions:11 interactions with chain H, 10 interactions with chain G,- Hydrophobic interactions: H:I.27, H:M.31, H:E.61, G:L.24, G:I.27, G:M.57, G:E.61
- Hydrogen bonds: H:Y.35, H:S.168, H:S.168, H:K.169, G:Y.35, G:Y.35
- Water bridges: H:R.20, H:N.32
- Salt bridges: H:R.20, H:K.50, G:R.20, G:H.28, G:K.169, G:K.169
FEC.67: 25 residues within 4Å:- Chain I: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, A.60, E.61, S.168, K.169
- Chain J: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
- Ligands: SO4.72
21 PLIP interactions:10 interactions with chain J, 11 interactions with chain I,- Hydrophobic interactions: J:I.27, J:M.31, J:E.61, I:L.24, I:I.27, I:M.31, I:I.54, I:E.61
- Hydrogen bonds: J:S.168, J:S.168, J:K.169, I:Y.35, I:Y.35
- Water bridges: J:R.20, J:N.32
- Salt bridges: J:R.20, J:K.50, I:R.20, I:H.28, I:K.169, I:K.169
FEC.90: 24 residues within 4Å:- Chain K: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169
- Chain L: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
- Ligands: SO4.86
21 PLIP interactions:12 interactions with chain L, 9 interactions with chain K,- Hydrophobic interactions: L:I.27, L:M.31, L:E.61, K:L.24, K:I.27, K:M.31, K:I.54, K:E.61
- Hydrogen bonds: L:Y.35, L:S.168, L:S.168, L:K.169, K:Y.35
- Water bridges: L:R.20, L:N.32
- Salt bridges: L:R.20, L:K.50, L:K.169, K:R.20, K:K.169, K:K.169
FEC.95: 23 residues within 4Å:- Chain M: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169
- Chain N: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
21 PLIP interactions:10 interactions with chain N, 11 interactions with chain M,- Hydrophobic interactions: N:I.27, N:M.31, N:E.61, M:L.24, M:I.27, M:I.27, M:M.31, M:I.54, M:E.61
- Hydrogen bonds: N:Y.35, N:S.168, N:S.168, N:K.169, M:Y.35
- Water bridges: N:N.32, M:N.32
- Salt bridges: N:R.20, N:K.50, M:R.20, M:K.169, M:K.169
FEC.115: 24 residues within 4Å:- Chain O: R.20, L.24, I.27, H.28, M.31, Y.35, K.50, I.54, M.57, E.61, S.168, K.169
- Chain P: R.20, I.27, H.28, M.31, Y.35, K.50, M.57, E.61, A.167, S.168, K.169
- Ligands: SO4.112
18 PLIP interactions:10 interactions with chain P, 8 interactions with chain O,- Hydrophobic interactions: P:I.27, P:M.31, P:M.57, P:E.61, O:L.24, O:M.31, O:I.54, O:E.61
- Hydrogen bonds: P:S.168, P:S.168, P:K.169, O:Y.35
- Water bridges: P:T.164, O:K.169
- Salt bridges: P:R.20, P:K.50, O:R.20, O:K.169
- 1 x 3PY: 3-HYDROXYPYRUVIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Macedo, S. et al., The nature of the di-iron site in the bacterioferritin fromDesulfovibrio desulfuricans. NAT.STRUCT.BIOL. (2003)
- Release Date
- 2003-04-01
- Peptides
- bacterioferritin: ABCDEFGHIJKLMNOP
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
NO
OP
P
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-16-mer
- Ligands
- 32 x FE: FE (III) ION(Non-covalent)
- 51 x SO4: SULFATE ION(Non-functional Binders)
- 24 x GOL: GLYCEROL(Non-functional Binders)
- 8 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Covalent)(Non-covalent)
- 1 x 3PY: 3-HYDROXYPYRUVIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Macedo, S. et al., The nature of the di-iron site in the bacterioferritin fromDesulfovibrio desulfuricans. NAT.STRUCT.BIOL. (2003)
- Release Date
- 2003-04-01
- Peptides
- bacterioferritin: ABCDEFGHIJKLMNOP
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
NO
OP
P