SMTL ID : 5xx9.1

Crystal structure of Bacterioferritin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-24-mer

Ligands

48 x FE2: FE (II) ION(Non-covalent)(Non-functional Binders)

FE2.1: 4 residues within 4Å: Chain A: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.18, A:E.18, A:E.51, A:E.51, A:E.127 FE2.2: 2 residues within 4Å: Chain A: N.23 Ligands: FE2.3 No protein-ligand interaction detected (PLIP) FE2.3: 2 residues within 4Å: Chain B: N.23 Ligands: FE2.2 No protein-ligand interaction detected (PLIP) FE2.4: 4 residues within 4Å: Chain B: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.18, B:E.18, B:E.51, B:E.127, B:E.127 FE2.5: 4 residues within 4Å: Chain C: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.18, C:E.18, C:E.51, C:E.127, C:E.127 FE2.6: 4 residues within 4Å: Chain C: M.52 Chain D: I.22, M.52 Ligands: FE2.8 No protein-ligand interaction detected (PLIP) FE2.7: 4 residues within 4Å: Chain D: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.18, D:E.18, D:E.51, D:E.127, D:E.127 FE2.8: 2 residues within 4Å: Chain C: N.23 Ligands: FE2.6 No protein-ligand interaction detected (PLIP) FE2.9: 4 residues within 4Å: Chain E: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.18, E:E.18, E:E.51, E:E.127, E:E.127 FE2.10: 4 residues within 4Å: Chain F: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.18, F:E.18, F:E.51, F:E.51, F:E.127 FE2.11: 2 residues within 4Å: Chain F: N.23 Ligands: FE2.12 No protein-ligand interaction detected (PLIP) FE2.12: 2 residues within 4Å: Chain G: N.23 Ligands: FE2.11 No protein-ligand interaction detected (PLIP) FE2.13: 4 residues within 4Å: Chain G: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.18, G:E.18, G:E.51, G:E.127, G:E.127 FE2.14: 4 residues within 4Å: Chain H: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.18, H:E.18, H:E.51, H:E.127, H:E.127 FE2.15: 4 residues within 4Å: Chain H: M.52 Chain I: I.22, M.52 Ligands: FE2.17 No protein-ligand interaction detected (PLIP) FE2.16: 4 residues within 4Å: Chain I: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.18, I:E.18, I:E.51, I:E.127, I:E.127 FE2.17: 2 residues within 4Å: Chain H: N.23 Ligands: FE2.15 No protein-ligand interaction detected (PLIP) FE2.18: 4 residues within 4Å: Chain J: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.18, J:E.18, J:E.51, J:E.127, J:E.127 FE2.19: 4 residues within 4Å: Chain K: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.18, K:E.18, K:E.51, K:E.51, K:E.127 FE2.20: 2 residues within 4Å: Chain K: N.23 Ligands: FE2.21 No protein-ligand interaction detected (PLIP) FE2.21: 2 residues within 4Å: Chain L: N.23 Ligands: FE2.20 No protein-ligand interaction detected (PLIP) FE2.22: 4 residues within 4Å: Chain L: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.18, L:E.18, L:E.51, L:E.127, L:E.127 FE2.23: 4 residues within 4Å: Chain M: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.18, M:E.18, M:E.51, M:E.127, M:E.127 FE2.24: 4 residues within 4Å: Chain M: M.52 Chain N: I.22, M.52 Ligands: FE2.26 No protein-ligand interaction detected (PLIP) FE2.25: 4 residues within 4Å: Chain N: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.18, N:E.18, N:E.51, N:E.127, N:E.127 FE2.26: 2 residues within 4Å: Chain M: N.23 Ligands: FE2.24 No protein-ligand interaction detected (PLIP) FE2.27: 4 residues within 4Å: Chain O: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.18, O:E.18, O:E.51, O:E.127, O:E.127 FE2.28: 4 residues within 4Å: Chain P: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.18, P:E.18, P:E.51, P:E.51, P:E.127 FE2.29: 2 residues within 4Å: Chain P: N.23 Ligands: FE2.30 No protein-ligand interaction detected (PLIP) FE2.30: 2 residues within 4Å: Chain Q: N.23 Ligands: FE2.29 No protein-ligand interaction detected (PLIP) FE2.31: 4 residues within 4Å: Chain Q: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.18, Q:E.18, Q:E.51, Q:E.127, Q:E.127 FE2.32: 4 residues within 4Å: Chain R: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.18, R:E.18, R:E.51, R:E.127, R:E.127 FE2.33: 4 residues within 4Å: Chain R: M.52 Chain S: I.22, M.52 Ligands: FE2.35 No protein-ligand interaction detected (PLIP) FE2.34: 4 residues within 4Å: Chain S: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.18, S:E.18, S:E.51, S:E.127, S:E.127 FE2.35: 2 residues within 4Å: Chain R: N.23 Ligands: FE2.33 No protein-ligand interaction detected (PLIP) FE2.36: 4 residues within 4Å: Chain T: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.18, T:E.18, T:E.51, T:E.127, T:E.127 FE2.37: 4 residues within 4Å: Chain U: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.18, U:E.18, U:E.51, U:E.127, U:E.127 FE2.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.39: 2 residues within 4Å: Chain J: L.19 Chain U: N.23 No protein-ligand interaction detected (PLIP) FE2.40: 4 residues within 4Å: Chain V: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.18, V:E.18, V:E.51, V:E.127, V:E.127 FE2.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.42: 2 residues within 4Å: Chain E: L.19 Chain V: N.23 No protein-ligand interaction detected (PLIP) FE2.43: 4 residues within 4Å: Chain W: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.18, W:E.18, W:E.51, W:E.127, W:E.127 FE2.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.45: 2 residues within 4Å: Chain T: L.19 Chain W: N.23 No protein-ligand interaction detected (PLIP) FE2.46: 4 residues within 4Å: Chain X: E.18, E.51, H.54, E.127 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.18, X:E.18, X:E.51, X:E.127, X:E.127 FE2.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.48: 2 residues within 4Å: Chain O: L.19 Chain X: N.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jobichen, C. et al., Bacterioferritin nanocage structures uncover the bio-mineralization process in ferritins. Pnas Nexus (2023)

Release Date

2018-07-11

Peptides

Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
A

G
B

H
C

I
D

J
F

K
A

L
B

M
C

N
D

O
F

P
A

Q
B

R
C

S
D

T
F

U
E

V
E

W
E

X
E

Bacterioferritin

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