SMTL ID : 6k43.1

Cryo-EM structure of Holo-bacterioferritin-form-I from Streptomyces coelicolor

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.51, A:E.51, A:H.54, A:E.127 FE2.3: 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 FE2.4: 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 FE2.6: 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.51, D:E.51, D:H.54, D:E.127 FE2.7: 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.51, E:E.51, E:H.54, E:E.127 FE2.9: 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.51, F:E.51, F:H.54, F:E.127 FE2.10: 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.51, G:E.51, G:H.54, G:E.127 FE2.11: 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.51, H:E.51, H:H.54, H:E.127 FE2.12: 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.51, I:E.51, I:H.54, I:E.127 FE2.13: 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 FE2.15: 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:H.54, K:E.127 FE2.16: 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 FE2.18: 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 FE2.20: 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.51, N:E.51, N:H.54, N:E.127 FE2.21: 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 FE2.23: 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 FE2.24: 3 residues within 4Å: Chain Q: E.47, E.51, H.130 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.47, Q:E.47, Q:E.51, Q:H.130 FE2.26: 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.51, R:E.51, R:H.54, R:E.127 FE2.27: 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.51, S:E.51, S:H.54, S:E.127 FE2.29: 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 FE2.31: 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.51, U:E.51, U:H.54, U:E.127 FE2.32: 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.51, V:E.51, V:H.54, V:E.127 FE2.34: 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.51, W:E.51, W:H.54, W:E.127 FE2.36: 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

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

HEM.2: 16 residues within 4Å: Chain A: L.19, I.22, N.23, F.26, R.45, F.49, M.52, E.56 Chain B: L.19, I.22, N.23, F.26, M.52, R.53, E.56, Y.71 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.26, B:F.26 pi-Stacking: A:F.49 HEM.5: 13 residues within 4Å: Chain C: I.22, F.26, R.45, F.49, M.52, R.53, H.54, E.56 Chain D: I.22, F.26, R.45, F.49, M.52 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:F.26, C:F.26, C:M.52, C:E.56, D:F.26 Hydrogen bonds: C:E.56 HEM.8: 16 residues within 4Å: Chain E: L.19, N.23, F.26, R.45, F.49, M.52, A.55, E.56, Y.71 Chain F: L.19, N.23, F.26, F.49, M.52, E.56, Y.71 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain F, Hydrophobic interactions: E:L.19, E:F.26, E:F.49, E:Y.71, F:L.19, F:F.26, F:Y.71 Salt bridges: E:R.45 HEM.14: 16 residues within 4Å: Chain J: L.19, I.22, N.23, F.26, F.49, M.52, E.56, Y.71 Chain K: I.22, N.23, F.26, R.45, F.49, M.52, R.53, E.56 7 PLIP interactions: 3 interactions with chain K, 4 interactions with chain J, Hydrophobic interactions: K:F.26, K:F.49, K:R.53, J:F.26, J:F.49, J:M.52 Hydrogen bonds: J:Y.71 HEM.17: 14 residues within 4Å: Chain L: L.19, F.26, R.45, F.49, M.52, R.53, E.56, Y.71 Chain M: L.19, N.23, F.26, F.49, M.52, Y.71 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain M, Hydrophobic interactions: L:F.26, M:F.26, M:F.26 Hydrogen bonds: L:Y.71 Salt bridges: L:R.53 pi-Stacking: M:F.49 HEM.19: 18 residues within 4Å: Chain H: L.19, I.22, N.23, F.26, M.52, R.53, A.55, E.56, V.57, Y.71 Chain N: L.19, N.23, F.26, R.45, F.49, M.52, E.56, Y.71 6 PLIP interactions: 2 interactions with chain H, 4 interactions with chain N, Hydrophobic interactions: H:R.53, H:E.56, N:L.19, N:F.26, N:Y.71 Hydrogen bonds: N:R.45 HEM.22: 16 residues within 4Å: Chain O: L.19, N.23, F.26, F.49, M.52, E.56, Y.71 Chain P: L.19, I.22, N.23, F.26, F.49, M.52, A.55, E.56, Y.71 11 PLIP interactions: 7 interactions with chain O, 4 interactions with chain P, Hydrophobic interactions: O:L.19, O:F.26, O:F.49, O:F.49, O:M.52, P:L.19, P:F.26, P:M.52 Hydrogen bonds: O:N.23, O:N.23, P:N.23 HEM.25: 14 residues within 4Å: Chain Q: L.19, 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, E.56 7 PLIP interactions: 3 interactions with chain Q, 4 interactions with chain R, Hydrophobic interactions: Q:F.26, R:L.19, R:F.26, R:F.49 Hydrogen bonds: Q:E.56, Q:Y.71 Salt bridges: R:R.45 HEM.28: 15 residues within 4Å: Chain I: L.19, N.23, F.26, M.52, E.56, Y.71 Chain S: L.19, I.22, N.23, F.26, R.45, F.49, M.52, E.56, Y.71 9 PLIP interactions: 6 interactions with chain S, 3 interactions with chain I, Hydrophobic interactions: S:F.26, S:F.49, S:F.49, S:Y.71, I:L.19, I:F.26, I:F.26 Salt bridges: S:R.45, S:R.45 HEM.30: 14 residues within 4Å: Chain T: L.19, N.23, F.26, F.49, M.52, E.56, Y.71 Chain U: L.19, I.22, N.23, F.26, R.45, M.52, E.56 3 PLIP interactions: 1 interactions with chain U, 2 interactions with chain T, Hydrophobic interactions: U:F.26, T:F.26 Hydrogen bonds: T:N.23 HEM.33: 17 residues within 4Å: Chain V: L.19, N.23, F.26, R.45, F.49, M.52, E.56, Y.71 Chain W: L.19, I.22, N.23, F.26, R.45, F.49, M.52, E.56, Y.71 6 PLIP interactions: 3 interactions with chain W, 3 interactions with chain V, Hydrophobic interactions: W:L.19, W:F.26, V:F.26, V:F.49 Salt bridges: W:R.45 Hydrogen bonds: V:Y.71 HEM.35: 14 residues within 4Å: Chain G: L.19, N.23, F.26, R.45, F.49, M.52, E.56 Chain X: L.19, N.23, F.26, F.49, M.52, E.56, Y.71 7 PLIP interactions: 2 interactions with chain X, 5 interactions with chain G, Hydrophobic interactions: X:F.26, X:Y.71, G:L.19, G:F.26, G:F.26, G:F.49 pi-Stacking: G:F.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jobichen, C. et al., Cryo-EM structure of Apo-bacterioferritin from Streptomyces coelicolor. To Be Published

Release Date

2021-02-03

Peptides

Bacterioferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
E

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

Related Entries With Identical Sequence