- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-24-mer
- Ligands
- 18 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 42 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.2: 7 residues within 4Å:- Chain A: K.2, G.3, D.4, V.111, H.112, D.113
- Chain D: R.102
Ligand excluded by PLIPMPD.3: 6 residues within 4Å:- Chain A: E.60, R.61, F.64
- Chain D: E.125, E.128, E.129
Ligand excluded by PLIPMPD.6: 9 residues within 4Å:- Chain B: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain F: R.102, E.128
Ligand excluded by PLIPMPD.7: 7 residues within 4Å:- Chain B: E.60, R.61, F.64, V.115
- Chain F: E.125, E.128, E.129
Ligand excluded by PLIPMPD.11: 7 residues within 4Å:- Chain C: E.60, R.61, F.64
- Chain Q: E.125, E.128, E.129, D.132
Ligand excluded by PLIPMPD.14: 9 residues within 4Å:- Chain D: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain S: R.102, E.128
Ligand excluded by PLIPMPD.15: 7 residues within 4Å:- Chain D: E.60, R.61, F.64, V.115
- Chain S: E.125, E.128, D.132
Ligand excluded by PLIPMPD.19: 7 residues within 4Å:- Chain E: K.2, G.3, D.4, V.111, H.112, D.113
- Chain H: R.102
Ligand excluded by PLIPMPD.20: 6 residues within 4Å:- Chain E: E.60, R.61, F.64
- Chain H: E.125, E.128, E.129
Ligand excluded by PLIPMPD.23: 9 residues within 4Å:- Chain F: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain J: R.102, E.128
Ligand excluded by PLIPMPD.24: 7 residues within 4Å:- Chain F: E.60, R.61, F.64, V.115
- Chain J: E.125, E.128, E.129
Ligand excluded by PLIPMPD.28: 7 residues within 4Å:- Chain G: E.60, R.61, F.64
- Chain M: E.125, E.128, E.129, D.132
Ligand excluded by PLIPMPD.31: 9 residues within 4Å:- Chain H: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain O: R.102, E.128
Ligand excluded by PLIPMPD.32: 7 residues within 4Å:- Chain H: E.60, R.61, F.64, V.115
- Chain O: E.125, E.128, D.132
Ligand excluded by PLIPMPD.36: 7 residues within 4Å:- Chain I: K.2, G.3, D.4, V.111, H.112, D.113
- Chain L: R.102
Ligand excluded by PLIPMPD.37: 6 residues within 4Å:- Chain I: E.60, R.61, F.64
- Chain L: E.125, E.128, E.129
Ligand excluded by PLIPMPD.40: 9 residues within 4Å:- Chain B: R.102, E.128
- Chain J: K.2, G.3, D.4, L.65, V.111, H.112, D.113
Ligand excluded by PLIPMPD.41: 7 residues within 4Å:- Chain B: E.125, E.128, E.129
- Chain J: E.60, R.61, F.64, V.115
Ligand excluded by PLIPMPD.45: 7 residues within 4Å:- Chain K: E.60, R.61, F.64
- Chain U: E.125, E.128, E.129, D.132
Ligand excluded by PLIPMPD.48: 9 residues within 4Å:- Chain L: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain W: R.102, E.128
Ligand excluded by PLIPMPD.49: 7 residues within 4Å:- Chain L: E.60, R.61, F.64, V.115
- Chain W: E.125, E.128, D.132
Ligand excluded by PLIPMPD.53: 7 residues within 4Å:- Chain M: K.2, G.3, D.4, V.111, H.112, D.113
- Chain P: R.102
Ligand excluded by PLIPMPD.54: 6 residues within 4Å:- Chain M: E.60, R.61, F.64
- Chain P: E.125, E.128, E.129
Ligand excluded by PLIPMPD.57: 9 residues within 4Å:- Chain N: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain R: R.102, E.128
Ligand excluded by PLIPMPD.58: 7 residues within 4Å:- Chain N: E.60, R.61, F.64, V.115
- Chain R: E.125, E.128, E.129
Ligand excluded by PLIPMPD.62: 7 residues within 4Å:- Chain E: E.125, E.128, E.129, D.132
- Chain O: E.60, R.61, F.64
Ligand excluded by PLIPMPD.65: 9 residues within 4Å:- Chain G: R.102, E.128
- Chain P: K.2, G.3, D.4, L.65, V.111, H.112, D.113
Ligand excluded by PLIPMPD.66: 7 residues within 4Å:- Chain G: E.125, E.128, D.132
- Chain P: E.60, R.61, F.64, V.115
Ligand excluded by PLIPMPD.70: 7 residues within 4Å:- Chain Q: K.2, G.3, D.4, V.111, H.112, D.113
- Chain T: R.102
Ligand excluded by PLIPMPD.71: 6 residues within 4Å:- Chain Q: E.60, R.61, F.64
- Chain T: E.125, E.128, E.129
Ligand excluded by PLIPMPD.74: 9 residues within 4Å:- Chain R: K.2, G.3, D.4, L.65, V.111, H.112, D.113
- Chain V: R.102, E.128
Ligand excluded by PLIPMPD.75: 7 residues within 4Å:- Chain R: E.60, R.61, F.64, V.115
- Chain V: E.125, E.128, E.129
Ligand excluded by PLIPMPD.79: 7 residues within 4Å:- Chain A: E.125, E.128, E.129, D.132
- Chain S: E.60, R.61, F.64
Ligand excluded by PLIPMPD.82: 9 residues within 4Å:- Chain C: R.102, E.128
- Chain T: K.2, G.3, D.4, L.65, V.111, H.112, D.113
Ligand excluded by PLIPMPD.83: 7 residues within 4Å:- Chain C: E.125, E.128, D.132
- Chain T: E.60, R.61, F.64, V.115
Ligand excluded by PLIPMPD.87: 7 residues within 4Å:- Chain U: K.2, G.3, D.4, V.111, H.112, D.113
- Chain X: R.102
Ligand excluded by PLIPMPD.88: 6 residues within 4Å:- Chain U: E.60, R.61, F.64
- Chain X: E.125, E.128, E.129
Ligand excluded by PLIPMPD.91: 9 residues within 4Å:- Chain N: R.102, E.128
- Chain V: K.2, G.3, D.4, L.65, V.111, H.112, D.113
Ligand excluded by PLIPMPD.92: 7 residues within 4Å:- Chain N: E.125, E.128, E.129
- Chain V: E.60, R.61, F.64, V.115
Ligand excluded by PLIPMPD.96: 7 residues within 4Å:- Chain I: E.125, E.128, E.129, D.132
- Chain W: E.60, R.61, F.64
Ligand excluded by PLIPMPD.99: 9 residues within 4Å:- Chain K: R.102, E.128
- Chain X: K.2, G.3, D.4, L.65, V.111, H.112, D.113
Ligand excluded by PLIPMPD.100: 7 residues within 4Å:- Chain K: E.125, E.128, D.132
- Chain X: E.60, R.61, F.64, V.115
Ligand excluded by PLIP- 24 x NA: SODIUM ION(Non-functional Binders)
NA.4: 2 residues within 4Å:- Chain A: T.136
- Chain G: D.34
Ligand excluded by PLIPNA.8: 3 residues within 4Å:- Chain B: D.132, T.136
- Chain I: D.34
Ligand excluded by PLIPNA.12: 3 residues within 4Å:- Chain C: D.132, T.136
- Chain D: D.34
Ligand excluded by PLIPNA.16: 3 residues within 4Å:- Chain B: D.34
- Chain D: D.132, T.136
Ligand excluded by PLIPNA.21: 2 residues within 4Å:- Chain E: T.136
- Chain K: D.34
Ligand excluded by PLIPNA.25: 3 residues within 4Å:- Chain A: D.34
- Chain F: D.132, T.136
Ligand excluded by PLIPNA.29: 3 residues within 4Å:- Chain G: D.132, T.136
- Chain H: D.34
Ligand excluded by PLIPNA.33: 3 residues within 4Å:- Chain F: D.34
- Chain H: D.132, T.136
Ligand excluded by PLIPNA.38: 2 residues within 4Å:- Chain C: D.34
- Chain I: T.136
Ligand excluded by PLIPNA.42: 3 residues within 4Å:- Chain E: D.34
- Chain J: D.132, T.136
Ligand excluded by PLIPNA.46: 3 residues within 4Å:- Chain K: D.132, T.136
- Chain L: D.34
Ligand excluded by PLIPNA.50: 3 residues within 4Å:- Chain J: D.34
- Chain L: D.132, T.136
Ligand excluded by PLIPNA.55: 2 residues within 4Å:- Chain M: T.136
- Chain S: D.34
Ligand excluded by PLIPNA.59: 3 residues within 4Å:- Chain N: D.132, T.136
- Chain U: D.34
Ligand excluded by PLIPNA.63: 3 residues within 4Å:- Chain O: D.132, T.136
- Chain P: D.34
Ligand excluded by PLIPNA.67: 3 residues within 4Å:- Chain N: D.34
- Chain P: D.132, T.136
Ligand excluded by PLIPNA.72: 2 residues within 4Å:- Chain Q: T.136
- Chain W: D.34
Ligand excluded by PLIPNA.76: 3 residues within 4Å:- Chain M: D.34
- Chain R: D.132, T.136
Ligand excluded by PLIPNA.80: 3 residues within 4Å:- Chain S: D.132, T.136
- Chain T: D.34
Ligand excluded by PLIPNA.84: 3 residues within 4Å:- Chain R: D.34
- Chain T: D.132, T.136
Ligand excluded by PLIPNA.89: 2 residues within 4Å:- Chain O: D.34
- Chain U: T.136
Ligand excluded by PLIPNA.93: 3 residues within 4Å:- Chain Q: D.34
- Chain V: D.132, T.136
Ligand excluded by PLIPNA.97: 3 residues within 4Å:- Chain W: D.132, T.136
- Chain X: D.34
Ligand excluded by PLIPNA.101: 3 residues within 4Å:- Chain V: D.34
- Chain X: D.132, T.136
Ligand excluded by PLIP- 6 x K: POTASSIUM ION(Non-covalent)
K.5: 8 residues within 4Å:- Chain B: N.148, Q.151
- Chain C: N.148, Q.151
- Chain D: N.148, Q.151
- Chain I: N.148, Q.151
No protein-ligand interaction detected (PLIP)K.22: 8 residues within 4Å:- Chain A: N.148, Q.151
- Chain F: N.148, Q.151
- Chain G: N.148, Q.151
- Chain H: N.148, Q.151
No protein-ligand interaction detected (PLIP)K.39: 8 residues within 4Å:- Chain E: N.148, Q.151
- Chain J: N.148, Q.151
- Chain K: N.148, Q.151
- Chain L: N.148, Q.151
No protein-ligand interaction detected (PLIP)K.56: 8 residues within 4Å:- Chain N: N.148, Q.151
- Chain O: N.148, Q.151
- Chain P: N.148, Q.151
- Chain U: N.148, Q.151
No protein-ligand interaction detected (PLIP)K.73: 8 residues within 4Å:- Chain M: N.148, Q.151
- Chain R: N.148, Q.151
- Chain S: N.148, Q.151
- Chain T: N.148, Q.151
No protein-ligand interaction detected (PLIP)K.90: 8 residues within 4Å:- Chain Q: N.148, Q.151
- Chain V: N.148, Q.151
- Chain W: N.148, Q.151
- Chain X: N.148, Q.151
No protein-ligand interaction detected (PLIP)- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.9: 10 residues within 4Å:- Chain B: R.117, D.118, K.121
- Chain F: R.117, D.118, K.121
- Chain J: D.118, K.121
- Ligands: SO4.26, SO4.43
No protein-ligand interaction detected (PLIP)SO4.17: 8 residues within 4Å:- Chain A: R.117, D.118, K.121
- Chain D: R.117, K.121
- Chain S: R.117, D.118, K.121
11 PLIP interactions:3 interactions with chain D, 4 interactions with chain S, 4 interactions with chain A- Water bridges: D:R.117, S:R.117, A:R.117
- Salt bridges: D:R.117, D:K.121, S:R.117, S:K.121, A:R.117, A:K.121
- Hydrogen bonds: S:D.118, A:D.118
SO4.26: 10 residues within 4Å:- Chain B: D.118, K.121
- Chain F: R.117, D.118, K.121
- Chain J: R.117, D.118, K.121
- Ligands: SO4.9, SO4.43
No protein-ligand interaction detected (PLIP)SO4.34: 8 residues within 4Å:- Chain E: R.117, D.118, K.121
- Chain H: R.117, K.121
- Chain O: R.117, D.118, K.121
11 PLIP interactions:4 interactions with chain E, 4 interactions with chain O, 3 interactions with chain H- Hydrogen bonds: E:D.118, O:D.118
- Water bridges: E:R.117, O:R.117, H:R.117
- Salt bridges: E:R.117, E:K.121, O:R.117, O:K.121, H:R.117, H:K.121
SO4.43: 10 residues within 4Å:- Chain B: R.117, D.118, K.121
- Chain F: D.118, K.121
- Chain J: R.117, D.118, K.121
- Ligands: SO4.9, SO4.26
No protein-ligand interaction detected (PLIP)SO4.51: 8 residues within 4Å:- Chain I: R.117, D.118, K.121
- Chain L: R.117, K.121
- Chain W: R.117, D.118, K.121
11 PLIP interactions:4 interactions with chain I, 4 interactions with chain W, 3 interactions with chain L- Hydrogen bonds: I:D.118, W:D.118
- Water bridges: I:R.117, W:R.117, L:R.117
- Salt bridges: I:R.117, I:K.121, W:R.117, W:K.121, L:R.117, L:K.121
SO4.60: 10 residues within 4Å:- Chain N: R.117, D.118, K.121
- Chain R: R.117, D.118, K.121
- Chain V: D.118, K.121
- Ligands: SO4.77, SO4.94
No protein-ligand interaction detected (PLIP)SO4.68: 8 residues within 4Å:- Chain G: R.117, D.118, K.121
- Chain M: R.117, D.118, K.121
- Chain P: R.117, K.121
11 PLIP interactions:3 interactions with chain P, 4 interactions with chain G, 4 interactions with chain M- Water bridges: P:R.117, G:R.117, M:R.117
- Salt bridges: P:R.117, P:K.121, G:R.117, G:K.121, M:R.117, M:K.121
- Hydrogen bonds: G:D.118, M:D.118
SO4.77: 10 residues within 4Å:- Chain N: D.118, K.121
- Chain R: R.117, D.118, K.121
- Chain V: R.117, D.118, K.121
- Ligands: SO4.60, SO4.94
No protein-ligand interaction detected (PLIP)SO4.85: 8 residues within 4Å:- Chain C: R.117, D.118, K.121
- Chain Q: R.117, D.118, K.121
- Chain T: R.117, K.121
11 PLIP interactions:4 interactions with chain Q, 3 interactions with chain T, 4 interactions with chain C- Hydrogen bonds: Q:D.118, C:D.118
- Water bridges: Q:R.117, T:R.117, C:R.117
- Salt bridges: Q:R.117, Q:K.121, T:R.117, T:K.121, C:R.117, C:K.121
SO4.94: 10 residues within 4Å:- Chain N: R.117, D.118, K.121
- Chain R: D.118, K.121
- Chain V: R.117, D.118, K.121
- Ligands: SO4.60, SO4.77
No protein-ligand interaction detected (PLIP)SO4.102: 8 residues within 4Å:- Chain K: R.117, D.118, K.121
- Chain U: R.117, D.118, K.121
- Chain X: R.117, K.121
11 PLIP interactions:4 interactions with chain K, 4 interactions with chain U, 3 interactions with chain X- Hydrogen bonds: K:D.118, U:D.118
- Water bridges: K:R.117, U:R.117, X:R.117
- Salt bridges: K:R.117, K:K.121, U:R.117, U:K.121, X:R.117, X:K.121
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yao, H. et al., Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry (2015)
- Release Date
- 2015-02-11
- Peptides
- Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
DM
AN
BO
CP
DQ
AR
BS
CT
DU
AV
BW
CX
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-24-mer
- Ligands
- 18 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 42 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 24 x NA: SODIUM ION(Non-functional Binders)
- 6 x K: POTASSIUM ION(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yao, H. et al., Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry (2015)
- Release Date
- 2015-02-11
- Peptides
- Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
DM
AN
BO
CP
DQ
AR
BS
CT
DU
AV
BW
CX
D