SMTL ID : 7y6f.1

Cryo-EM structure of Apo form of ScBfr

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

24 x FE2: FE (II) ION(Non-covalent)

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:H.54, A:E.127 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:H.54, B:E.127 FE2.6: 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:H.54, C:E.127 FE2.9: 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:H.54, D:E.127 FE2.11: 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:H.54, E:E.127 FE2.14: 4 residues within 4Å: Chain F: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.51, F:E.94, F:E.127 FE2.16: 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:H.54, G:E.127 FE2.19: 4 residues within 4Å: Chain H: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.18, H:E.18, H:E.51, H:E.127 FE2.23: 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:H.54, I:E.127 FE2.24: 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:H.54, J:E.127 FE2.26: 4 residues within 4Å: Chain K: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.51, K:E.94, K:E.127 FE2.29: 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:H.54, L:E.127 FE2.32: 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:H.54, M:E.127 FE2.34: 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:H.54, N:E.127 FE2.36: 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:H.54, O:E.127 FE2.37: 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:H.54, P:E.127 FE2.40: 4 residues within 4Å: Chain Q: E.51, E.94, E.127, H.130 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.127 FE2.43: 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:H.54, R:E.127 FE2.45: 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:H.54, S:E.127 FE2.50: 4 residues within 4Å: Chain T: E.51, E.94, E.127, H.130 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:E.51, T:E.127 FE2.51: 4 residues within 4Å: Chain U: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.18, U:E.18, U:E.51, U:E.127 FE2.54: 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:H.54, V:E.127 FE2.55: 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:H.54, W:E.127 FE2.59: 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:H.54, X:E.127

23 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: Y.25, E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.51, A:E.94, A:E.127 FE.5: 4 residues within 4Å: Chain B: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.51, B:E.94, B:E.127 FE.7: 2 residues within 4Å: Chain C: A.21, A.97 No protein-ligand interaction detected (PLIP) FE.10: 4 residues within 4Å: Chain D: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.51, D:E.94, D:E.127 FE.12: 4 residues within 4Å: Chain E: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.51, E:E.94, E:E.127 FE.13: 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:H.54, F:E.127 FE.17: 4 residues within 4Å: Chain G: E.51, E.94, E.127, H.130 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.51, G:E.94, G:E.94, G:E.127 FE.20: 5 residues within 4Å: Chain H: Y.25, E.51, E.94, E.127, H.130 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.51, H:E.94, H:E.94, H:E.127 FE.22: 4 residues within 4Å: Chain I: E.51, E.94, E.127, H.130 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.51, I:E.94, I:E.94, I:E.127 FE.25: 5 residues within 4Å: Chain J: Y.25, E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.51, J:E.94, J:E.127 FE.27: 4 residues within 4Å: Chain K: E.18, E.51, H.54, E.127 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.18, K:E.18, K:E.51, K:E.127 FE.30: 4 residues within 4Å: Chain L: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.51, L:E.94, L:E.127 FE.33: 5 residues within 4Å: Chain M: Y.25, E.51, E.94, E.127, H.130 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:E.51, M:E.94, M:E.94, M:E.127 FE.35: 4 residues within 4Å: Chain O: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.51, O:E.94, O:E.127 FE.38: 4 residues within 4Å: Chain P: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.51, P:E.94, P:E.127 FE.41: 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:H.54, Q:E.127 FE.44: 4 residues within 4Å: Chain R: E.51, E.94, E.127, H.130 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:E.51, R:E.94, R:E.94, R:E.127 FE.46: 4 residues within 4Å: Chain S: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.51, S:E.94, S:E.127 FE.48: 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:H.54, T:E.127 FE.52: 4 residues within 4Å: Chain U: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.51, U:E.94, U:E.127 FE.53: 4 residues within 4Å: Chain V: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.51, V:E.94, V:E.127 FE.56: 5 residues within 4Å: Chain W: Y.25, E.51, E.94, E.127, H.130 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.51, W:E.94, W:E.94, W:E.127 FE.58: 4 residues within 4Å: Chain X: E.51, E.94, E.127, H.130 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.51, X:E.94, X:E.127

12 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)

HEM.3: 11 residues within 4Å: Chain A: L.19, N.23, F.26, M.52, E.56, Y.71 Chain B: L.19, N.23, F.26, M.52, Y.71 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.26, A:M.52, B:F.26 pi-Stacking: A:F.49 HEM.8: 15 residues within 4Å: Chain C: I.22, N.23, F.26, R.45, F.49, M.52, R.53, H.54, E.56 Chain D: F.26, R.45, F.49, M.52, E.56, Y.71 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D, Hydrophobic interactions: C:F.26, C:F.26, C:M.52, C:E.56, D:F.26, D:M.52 Hydrogen bonds: C:E.56, C:E.56 HEM.15: 15 residues within 4Å: Chain E: L.19, N.23, F.26, F.49, M.52, E.56, Y.71 Chain F: L.19, N.23, F.26, R.45, F.49, M.52, R.53, Y.71 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain F, Hydrophobic interactions: E:L.19, E:F.26, E:M.52, E:E.56, E:Y.71, F:F.26, F:F.26, F:F.49, F:F.49 Salt bridges: F:K.30, F:R.45 HEM.18: 9 residues within 4Å: Chain G: L.19, F.26, F.49, M.52, E.56 Chain X: N.23, F.26, F.49, M.52 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain X, Hydrophobic interactions: G:F.26, G:F.49, G:M.52, G:E.56, X:F.26, X:F.49 Salt bridges: G:R.53 HEM.21: 14 residues within 4Å: Chain H: L.19, N.23, F.26, F.49, M.52, R.53, A.55, E.56, V.57 Chain N: F.26, R.45, F.49, M.52, Y.71 14 PLIP interactions: 4 interactions with chain N, 10 interactions with chain H, Hydrophobic interactions: N:F.26, N:M.52, N:Y.71, H:L.19, H:F.26, H:F.26, H:F.49, H:F.49, H:M.52, H:R.53, H:A.55, H:E.56 Hydrogen bonds: N:R.45, H:R.53 HEM.28: 19 residues within 4Å: Chain J: L.19, I.22, N.23, F.26, R.45, F.49, M.52, A.55, E.56, Y.71 Chain K: I.22, N.23, F.26, R.45, F.49, M.52, R.53, A.55, E.56 6 PLIP interactions: 3 interactions with chain K, 3 interactions with chain J, Hydrophobic interactions: K:F.26, K:M.52, K:E.56, J:F.26, J:F.49, J:M.52 HEM.31: 20 residues within 4Å: Chain L: L.19, I.22, N.23, F.26, R.45, M.52, R.53, A.55, E.56, T.59, Y.71 Chain M: L.19, I.22, N.23, F.26, R.45, F.49, M.52, E.56, Y.71 15 PLIP interactions: 11 interactions with chain L, 4 interactions with chain M, Hydrophobic interactions: L:L.19, L:I.22, L:F.26, L:F.26, L:R.53, L:A.55, M:L.19, M:F.26, M:F.26 Hydrogen bonds: L:M.52, L:R.53, L:E.56, L:T.59, L:Y.71, M:R.45 HEM.39: 19 residues within 4Å: Chain O: L.19, I.22, N.23, F.26, R.45, M.52, A.55, E.56, Y.71 Chain P: L.19, I.22, N.23, F.26, R.45, M.52, R.53, A.55, E.56, Y.71 9 PLIP interactions: 5 interactions with chain O, 4 interactions with chain P, Hydrophobic interactions: O:L.19, O:F.26, O:F.26, P:L.19, P:F.26, P:M.52 Hydrogen bonds: O:N.23, O:N.23, P:N.23 HEM.42: 18 residues within 4Å: Chain Q: L.19, I.22, N.23, F.26, R.45, M.52, E.56, Y.71 Chain R: L.19, N.23, F.26, R.45, F.49, M.52, R.53, A.55, E.56, Y.71 11 PLIP interactions: 3 interactions with chain Q, 8 interactions with chain R, Hydrophobic interactions: Q:I.22, Q:F.26, Q:M.52, R:L.19, R:F.26, R:F.49, R:F.49, R:M.52, R:Y.71 Salt bridges: R:K.30, R:R.45 HEM.47: 10 residues within 4Å: Chain I: L.19, F.26, F.49, M.52, E.56 Chain S: N.23, F.26, R.45, F.49, M.52 13 PLIP interactions: 6 interactions with chain I, 7 interactions with chain S, Hydrophobic interactions: I:L.19, I:F.26, I:F.26, I:F.26, I:F.49, I:E.56, S:F.26, S:F.26, S:F.49, S:F.49, S:M.52 Salt bridges: S:R.45, S:R.45 HEM.49: 16 residues within 4Å: Chain T: L.19, N.23, F.26, R.45, F.49, M.52, A.55, E.56, Y.71 Chain U: L.19, I.22, N.23, F.26, R.45, M.52, E.56 8 PLIP interactions: 3 interactions with chain T, 5 interactions with chain U, Hydrophobic interactions: T:F.26, T:M.52, T:Y.71, U:I.22, U:F.26, U:F.26, U:M.52 pi-Stacking: U:F.26 HEM.57: 17 residues within 4Å: Chain V: L.19, N.23, F.26, R.45, M.52, A.55, E.56, T.59, Y.71 Chain W: L.19, N.23, F.26, R.45, F.49, M.52, E.56, Y.71 11 PLIP interactions: 6 interactions with chain W, 5 interactions with chain V, Hydrophobic interactions: W:L.19, W:F.26, W:F.49, W:F.49, W:Y.71, V:L.19, V:F.26, V:F.26, V:M.52 Salt bridges: W:R.45 Hydrogen bonds: V:T.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-07-05

Peptides

Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Bacterioferritin

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