SMTL ID : 2htn.1

E. coli bacterioferritin in its as-isolated form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.18, E.51, H.54, E.127 Ligands: FE.2 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 FE.2: 5 residues within 4Å: Chain A: E.51, E.94, E.127, H.130 Ligands: FE.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.51, A:E.94, A:E.94, A:E.127, A:H.130 FE.4: 5 residues within 4Å: Chain B: E.18, E.51, H.54, E.127 Ligands: FE.5 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 FE.5: 5 residues within 4Å: Chain B: E.51, E.94, E.127, H.130 Ligands: FE.4 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.51, B:E.94, B:E.94, B:E.127, B:H.130 FE.6: 5 residues within 4Å: Chain C: E.18, E.51, H.54, E.127 Ligands: FE.7 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 FE.7: 5 residues within 4Å: Chain C: E.51, E.94, E.127, H.130 Ligands: FE.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.51, C:E.51, C:E.94, C:E.127, C:H.130 FE.9: 5 residues within 4Å: Chain D: E.18, E.51, H.54, E.127 Ligands: FE.10 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.18, D:E.51, D:H.54, D:E.127, D:E.127 FE.10: 5 residues within 4Å: Chain D: E.51, E.94, E.127, H.130 Ligands: FE.9 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.51, D:E.94, D:E.94, D:E.127, D:H.130 FE.11: 5 residues within 4Å: Chain E: E.18, E.51, H.54, E.127 Ligands: FE.12 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 FE.12: 5 residues within 4Å: Chain E: E.51, E.94, E.127, H.130 Ligands: FE.11 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.94, E:E.94, E:E.127, E:H.130, H2O.3 FE.14: 5 residues within 4Å: Chain F: E.18, E.51, H.54, E.127 Ligands: FE.15 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.15: 5 residues within 4Å: Chain F: E.51, E.94, E.127, H.130 Ligands: FE.14 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.51, F:E.94, F:E.94, F:E.127, F:H.130 FE.16: 5 residues within 4Å: Chain G: E.18, E.51, H.54, E.127 Ligands: FE.17 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 FE.17: 5 residues within 4Å: Chain G: E.51, E.94, E.127, H.130 Ligands: FE.16 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.51, G:E.94, G:E.94, G:E.127, G:H.130 FE.19: 5 residues within 4Å: Chain H: E.18, E.51, H.54, E.127 Ligands: FE.20 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.18, H:E.18, H:E.51, H:H.54, H:E.127 FE.20: 5 residues within 4Å: Chain H: E.51, E.94, E.127, H.130 Ligands: FE.19 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.51, H:E.94, H:E.94, H:E.127, H:H.130 FE.21: 5 residues within 4Å: Chain I: E.18, E.51, H.54, E.127 Ligands: FE.22 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 FE.22: 5 residues within 4Å: Chain I: E.51, E.94, E.127, H.130 Ligands: FE.21 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.51, I:E.94, I:E.94, I:E.127, I:H.130 FE.24: 5 residues within 4Å: Chain J: E.18, E.51, H.54, E.127 Ligands: FE.25 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 FE.25: 5 residues within 4Å: Chain J: E.51, E.94, E.127, H.130 Ligands: FE.24 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.51, J:E.94, J:E.94, J:E.127, J:H.130 FE.26: 5 residues within 4Å: Chain K: E.18, E.51, H.54, E.127 Ligands: FE.27 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 FE.27: 5 residues within 4Å: Chain K: E.51, E.94, E.127, H.130 Ligands: FE.26 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.51, K:E.51, K:E.94, K:E.127, K:H.130 FE.29: 5 residues within 4Å: Chain L: E.18, E.51, H.54, E.127 Ligands: FE.30 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.18, L:E.51, L:H.54, L:E.127, L:E.127 FE.30: 5 residues within 4Å: Chain L: E.51, E.94, E.127, H.130 Ligands: FE.29 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.51, L:E.94, L:E.94, L:E.127, L:H.130 FE.31: 5 residues within 4Å: Chain M: E.18, E.51, H.54, E.127 Ligands: FE.32 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 FE.32: 5 residues within 4Å: Chain M: E.51, E.94, E.127, H.130 Ligands: FE.31 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.94, M:E.94, M:E.127, M:H.130, H2O.7 FE.34: 5 residues within 4Å: Chain N: E.18, E.51, H.54, E.127 Ligands: FE.35 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 FE.35: 5 residues within 4Å: Chain N: E.51, E.94, E.127, H.130 Ligands: FE.34 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.51, N:E.94, N:E.94, N:E.127, N:H.130 FE.36: 5 residues within 4Å: Chain O: E.18, E.51, H.54, E.127 Ligands: FE.37 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 FE.37: 5 residues within 4Å: Chain O: E.51, E.94, E.127, H.130 Ligands: FE.36 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.51, O:E.94, O:E.94, O:E.127, O:H.130 FE.39: 5 residues within 4Å: Chain P: E.18, E.51, H.54, E.127 Ligands: FE.40 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 FE.40: 5 residues within 4Å: Chain P: E.51, E.94, E.127, H.130 Ligands: FE.39 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.51, P:E.94, P:E.94, P:E.127, P:H.130 FE.41: 5 residues within 4Å: Chain Q: E.18, E.51, H.54, E.127 Ligands: FE.42 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.42: 5 residues within 4Å: Chain Q: E.51, E.94, E.127, H.130 Ligands: FE.41 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.51, Q:E.94, Q:E.94, Q:E.127, Q:H.130 FE.44: 5 residues within 4Å: Chain R: E.18, E.51, H.54, E.127 Ligands: FE.45 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 FE.45: 5 residues within 4Å: Chain R: E.51, E.94, E.127, H.130 Ligands: FE.44 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.51, R:E.94, R:E.94, R:E.127, R:H.130 FE.46: 5 residues within 4Å: Chain S: E.18, E.51, H.54, E.127 Ligands: FE.47 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 FE.47: 5 residues within 4Å: Chain S: E.51, E.94, E.127, H.130 Ligands: FE.46 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.51, S:E.51, S:E.94, S:E.127, S:H.130 FE.49: 5 residues within 4Å: Chain T: E.18, E.51, H.54, E.127 Ligands: FE.50 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.18, T:E.51, T:H.54, T:E.127, T:E.127 FE.50: 5 residues within 4Å: Chain T: E.51, E.94, E.127, H.130 Ligands: FE.49 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.51, T:E.94, T:E.94, T:E.127, T:H.130 FE.51: 5 residues within 4Å: Chain U: E.18, E.51, H.54, E.127 Ligands: FE.52 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.18, U:E.18, U:E.51, U:H.54, U:E.127 FE.52: 5 residues within 4Å: Chain U: E.51, E.94, E.127, H.130 Ligands: FE.51 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.94, U:E.94, U:E.127, U:H.130, H2O.10 FE.54: 5 residues within 4Å: Chain V: E.18, E.51, H.54, E.127 Ligands: FE.55 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 FE.55: 5 residues within 4Å: Chain V: E.51, E.94, E.127, H.130 Ligands: FE.54 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.51, V:E.94, V:E.94, V:E.127, V:H.130 FE.56: 5 residues within 4Å: Chain W: E.18, E.51, H.54, E.127 Ligands: FE.57 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 FE.57: 5 residues within 4Å: Chain W: E.51, E.94, E.127, H.130 Ligands: FE.56 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.51, W:E.94, W:E.94, W:E.127, W:H.130 FE.59: 5 residues within 4Å: Chain X: E.18, E.51, H.54, E.127 Ligands: FE.60 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 FE.60: 5 residues within 4Å: Chain X: E.51, E.94, E.127, H.130 Ligands: FE.59 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.51, X:E.94, X:E.94, X:E.127, X:H.130

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

HEM.3: 17 residues within 4Å: Chain A: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain B: L.19, I.22, F.26, Y.45, I.49, M.52, K.53 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:L.19, B:F.26, B:F.26, B:Y.45, B:I.49, B:M.52, A:L.19, A:I.22, A:F.26, A:F.26, A:M.52, A:A.55 Salt bridges: B:K.53, A:K.53 HEM.8: 18 residues within 4Å: Chain C: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 16 PLIP interactions: 8 interactions with chain C, 8 interactions with chain D, Hydrophobic interactions: C:L.19, C:I.22, C:F.26, C:F.26, C:I.49, C:M.52, C:A.55, D:L.19, D:I.22, D:F.26, D:F.26, D:I.49, D:I.49, D:M.52 Salt bridges: C:K.53, D:K.53 HEM.13: 18 residues within 4Å: Chain E: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 18 PLIP interactions: 9 interactions with chain E, 9 interactions with chain F, Hydrophobic interactions: E:L.19, E:I.22, E:I.22, E:F.26, E:F.26, E:I.49, E:I.49, E:M.52, F:L.19, F:I.22, F:I.22, F:F.26, F:F.26, F:I.49, F:M.52, F:A.55 Salt bridges: E:K.53, F:K.53 HEM.18: 17 residues within 4Å: Chain G: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 14 PLIP interactions: 7 interactions with chain H, 7 interactions with chain G, Hydrophobic interactions: H:L.19, H:I.22, H:F.26, H:F.26, H:I.49, H:M.52, G:L.19, G:I.22, G:F.26, G:F.26, G:M.52, G:A.55 Salt bridges: H:K.53, G:K.53 HEM.23: 17 residues within 4Å: Chain I: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain J: L.19, I.22, F.26, Y.45, I.49, M.52, K.53 14 PLIP interactions: 7 interactions with chain I, 7 interactions with chain J, Hydrophobic interactions: I:L.19, I:I.22, I:F.26, I:F.26, I:M.52, I:A.55, J:L.19, J:F.26, J:F.26, J:Y.45, J:I.49, J:M.52 Salt bridges: I:K.53, J:K.53 HEM.28: 18 residues within 4Å: Chain K: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 16 PLIP interactions: 8 interactions with chain K, 8 interactions with chain L, Hydrophobic interactions: K:L.19, K:I.22, K:F.26, K:F.26, K:I.49, K:M.52, K:A.55, L:L.19, L:I.22, L:F.26, L:F.26, L:I.49, L:I.49, L:M.52 Salt bridges: K:K.53, L:K.53 HEM.33: 18 residues within 4Å: Chain M: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 18 PLIP interactions: 9 interactions with chain M, 9 interactions with chain N, Hydrophobic interactions: M:L.19, M:I.22, M:I.22, M:F.26, M:F.26, M:I.49, M:I.49, M:M.52, N:L.19, N:I.22, N:I.22, N:F.26, N:F.26, N:I.49, N:M.52, N:A.55 Salt bridges: M:K.53, N:K.53 HEM.38: 17 residues within 4Å: Chain O: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 14 PLIP interactions: 7 interactions with chain P, 7 interactions with chain O, Hydrophobic interactions: P:L.19, P:I.22, P:F.26, P:F.26, P:I.49, P:M.52, O:L.19, O:I.22, O:F.26, O:F.26, O:M.52, O:A.55 Salt bridges: P:K.53, O:K.53 HEM.43: 17 residues within 4Å: Chain Q: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain R: L.19, I.22, F.26, Y.45, I.49, M.52, K.53 14 PLIP interactions: 7 interactions with chain R, 7 interactions with chain Q, Hydrophobic interactions: R:L.19, R:F.26, R:F.26, R:Y.45, R:I.49, R:M.52, Q:L.19, Q:I.22, Q:F.26, Q:F.26, Q:M.52, Q:A.55 Salt bridges: R:K.53, Q:K.53 HEM.48: 18 residues within 4Å: Chain S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 16 PLIP interactions: 8 interactions with chain S, 8 interactions with chain T, Hydrophobic interactions: S:L.19, S:I.22, S:F.26, S:F.26, S:I.49, S:M.52, S:A.55, T:L.19, T:I.22, T:F.26, T:F.26, T:I.49, T:I.49, T:M.52 Salt bridges: S:K.53, T:K.53 HEM.53: 18 residues within 4Å: Chain U: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 18 PLIP interactions: 9 interactions with chain V, 9 interactions with chain U, Hydrophobic interactions: V:L.19, V:I.22, V:I.22, V:F.26, V:F.26, V:I.49, V:M.52, V:A.55, U:L.19, U:I.22, U:I.22, U:F.26, U:F.26, U:I.49, U:I.49, U:M.52 Salt bridges: V:K.53, U:K.53 HEM.58: 17 residues within 4Å: Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 14 PLIP interactions: 7 interactions with chain W, 7 interactions with chain X, Hydrophobic interactions: W:L.19, W:I.22, W:F.26, W:F.26, W:M.52, W:A.55, X:L.19, X:I.22, X:F.26, X:F.26, X:I.49, X:M.52 Salt bridges: W:K.53, X:K.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Eerde, A. et al., Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form. Acta Crystallogr.,Sect.F (2006)

Release Date

2006-11-21

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
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Q
A

R
B

S
C

T
D

U
E

V
F

W
G

X
H

Bacterioferritin

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