SMTL ID : 3bvk.1

Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-24-mer

Ligands

56 x FE: FE (III) ION(Non-covalent)(Non-functional Binders)

FE.1: 7 residues within 4Å: Chain A: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.31 FE.2: 6 residues within 4Å: Chain A: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.64, A:E.108, A:E.144 FE.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.4: 8 residues within 4Å: Chain B: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.31 FE.5: 5 residues within 4Å: Chain B: E.64, E.108, Q.141, E.144 Ligands: FE.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.64, B:E.108, B:E.144 FE.7: 7 residues within 4Å: Chain C: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.31 FE.8: 6 residues within 4Å: Chain C: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.64, C:E.108, C:E.144 FE.10: 8 residues within 4Å: Chain D: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.31 FE.11: 6 residues within 4Å: Chain D: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.64, D:E.108, D:E.144 FE.12: 8 residues within 4Å: Chain E: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.13 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.31 FE.13: 6 residues within 4Å: Chain E: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.12 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.64, E:E.108, E:E.144 FE.14: 3 residues within 4Å: Ligands: FE.31, FE.48, FE.65 No protein-ligand interaction detected (PLIP) FE.15: 7 residues within 4Å: Chain F: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.31 FE.16: 6 residues within 4Å: Chain F: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.15 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.64, F:E.108, F:E.144 FE.18: 7 residues within 4Å: Chain G: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.19 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.31 FE.19: 6 residues within 4Å: Chain G: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.18 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.64, G:E.108, G:E.144 FE.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.21: 8 residues within 4Å: Chain H: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.31 FE.22: 5 residues within 4Å: Chain H: E.64, E.108, Q.141, E.144 Ligands: FE.21 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.64, H:E.108, H:E.144 FE.24: 7 residues within 4Å: Chain I: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.25 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.31 FE.25: 6 residues within 4Å: Chain I: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.24 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.64, I:E.108, I:E.144 FE.27: 8 residues within 4Å: Chain J: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.28 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.31 FE.28: 6 residues within 4Å: Chain J: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.27 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.64, J:E.108, J:E.144 FE.29: 8 residues within 4Å: Chain K: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.30 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.31 FE.30: 6 residues within 4Å: Chain K: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.29 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.64, K:E.108, K:E.144 FE.31: 3 residues within 4Å: Ligands: FE.14, FE.48, FE.65 No protein-ligand interaction detected (PLIP) FE.32: 7 residues within 4Å: Chain L: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.33 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.31 FE.33: 6 residues within 4Å: Chain L: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.32 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.64, L:E.108, L:E.144 FE.35: 7 residues within 4Å: Chain M: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.36 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.31 FE.36: 6 residues within 4Å: Chain M: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.35 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.64, M:E.108, M:E.144 FE.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.38: 8 residues within 4Å: Chain N: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.39 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.31 FE.39: 5 residues within 4Å: Chain N: E.64, E.108, Q.141, E.144 Ligands: FE.38 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.64, N:E.108, N:E.144 FE.41: 7 residues within 4Å: Chain O: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.42 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:E.31 FE.42: 6 residues within 4Å: Chain O: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.41 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.64, O:E.108, O:E.144 FE.44: 8 residues within 4Å: Chain P: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.45 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:E.31 FE.45: 6 residues within 4Å: Chain P: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.44 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.64, P:E.108, P:E.144 FE.46: 8 residues within 4Å: Chain Q: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.47 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.31 FE.47: 6 residues within 4Å: Chain Q: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.46 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.64, Q:E.108, Q:E.144 FE.48: 3 residues within 4Å: Ligands: FE.14, FE.31, FE.65 No protein-ligand interaction detected (PLIP) FE.49: 7 residues within 4Å: Chain R: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.50 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.31 FE.50: 6 residues within 4Å: Chain R: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.49 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.64, R:E.108, R:E.144 FE.52: 7 residues within 4Å: Chain S: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.53 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:E.31 FE.53: 6 residues within 4Å: Chain S: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.52 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.64, S:E.108, S:E.144 FE.54: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.55: 8 residues within 4Å: Chain T: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.56 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.31 FE.56: 5 residues within 4Å: Chain T: E.64, E.108, Q.141, E.144 Ligands: FE.55 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.64, T:E.108, T:E.144 FE.58: 7 residues within 4Å: Chain U: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.59 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:E.31 FE.59: 6 residues within 4Å: Chain U: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.58 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.64, U:E.108, U:E.144 FE.61: 8 residues within 4Å: Chain V: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.62 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:E.31 FE.62: 6 residues within 4Å: Chain V: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.61 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.64, V:E.108, V:E.144 FE.63: 8 residues within 4Å: Chain W: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.64 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.31 FE.64: 6 residues within 4Å: Chain W: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.63 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.64, W:E.108, W:E.144 FE.65: 3 residues within 4Å: Ligands: FE.14, FE.31, FE.48 No protein-ligand interaction detected (PLIP) FE.66: 7 residues within 4Å: Chain X: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.67 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:E.31 FE.67: 6 residues within 4Å: Chain X: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.66 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.64, X:E.108, X:E.144

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain B: M.32, S.35, N.36, Y.65 Chain E: M.32, N.36, Y.65 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:M.32, E:N.36, B:S.35, B:S.35 Water bridges: E:Y.65, B:Y.65 GOL.9: 7 residues within 4Å: Chain C: M.32, S.35, N.36, Y.65 Chain D: M.32, Y.65, I.87 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.35, C:S.35, C:N.36 Water bridges: D:N.36, D:Y.65 GOL.17: 8 residues within 4Å: Chain A: M.32, S.35, N.36, Y.65 Chain F: M.32, S.35, N.36, Y.65 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:S.35, A:N.36, A:N.36, F:S.35, F:S.35 GOL.23: 7 residues within 4Å: Chain H: M.32, S.35, N.36, Y.65 Chain K: M.32, N.36, Y.65 6 PLIP interactions: 3 interactions with chain K, 3 interactions with chain H Hydrogen bonds: K:M.32, K:N.36, H:S.35, H:S.35 Water bridges: K:Y.65, H:Y.65 GOL.26: 7 residues within 4Å: Chain I: M.32, S.35, N.36, Y.65 Chain J: M.32, Y.65, I.87 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain I Water bridges: J:N.36, J:Y.65 Hydrogen bonds: I:S.35, I:S.35, I:N.36 GOL.34: 8 residues within 4Å: Chain G: M.32, S.35, N.36, Y.65 Chain L: M.32, S.35, N.36, Y.65 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain L Hydrogen bonds: G:S.35, G:N.36, G:N.36, L:S.35, L:S.35 GOL.40: 7 residues within 4Å: Chain N: M.32, S.35, N.36, Y.65 Chain Q: M.32, N.36, Y.65 6 PLIP interactions: 3 interactions with chain Q, 3 interactions with chain N Hydrogen bonds: Q:M.32, Q:N.36, N:S.35, N:S.35 Water bridges: Q:Y.65, N:Y.65 GOL.43: 7 residues within 4Å: Chain O: M.32, S.35, N.36, Y.65 Chain P: M.32, Y.65, I.87 5 PLIP interactions: 3 interactions with chain O, 2 interactions with chain P Hydrogen bonds: O:S.35, O:S.35, O:N.36 Water bridges: P:N.36, P:Y.65 GOL.51: 8 residues within 4Å: Chain M: M.32, S.35, N.36, Y.65 Chain R: M.32, S.35, N.36, Y.65 5 PLIP interactions: 3 interactions with chain M, 2 interactions with chain R Hydrogen bonds: M:S.35, M:N.36, M:N.36, R:S.35, R:S.35 GOL.57: 7 residues within 4Å: Chain T: M.32, S.35, N.36, Y.65 Chain W: M.32, N.36, Y.65 6 PLIP interactions: 3 interactions with chain W, 3 interactions with chain T Hydrogen bonds: W:M.32, W:N.36, T:S.35, T:S.35 Water bridges: W:Y.65, T:Y.65 GOL.60: 7 residues within 4Å: Chain U: M.32, S.35, N.36, Y.65 Chain V: M.32, Y.65, I.87 5 PLIP interactions: 3 interactions with chain U, 2 interactions with chain V Hydrogen bonds: U:S.35, U:S.35, U:N.36 Water bridges: V:N.36, V:Y.65 GOL.68: 8 residues within 4Å: Chain S: M.32, S.35, N.36, Y.65 Chain X: M.32, S.35, N.36, Y.65 5 PLIP interactions: 3 interactions with chain S, 2 interactions with chain X Hydrogen bonds: S:S.35, S:N.36, S:N.36, X:S.35, X:S.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, K.H. et al., Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin. To be Published

Release Date

2009-01-13

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Ferritin

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