SMTL ID : 3egm.1

Structural basis of iron transport gating in Helicobacter pylori ferritin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 8 residues within 4Å: Chain A: E.31, E.64, H.67, I.111, Y.137, 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: 5 residues within 4Å: Chain A: H.163 Chain B: H.163 Chain D: H.163, L.167 Chain O: H.163 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.163 FE.5: 7 residues within 4Å: Chain B: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.31 FE.6: 6 residues within 4Å: Chain B: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.64, B:E.108, B:E.144 FE.8: 7 residues within 4Å: Chain C: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.31 FE.9: 6 residues within 4Å: Chain C: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.8 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 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.31, D:H.67 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.13: 7 residues within 4Å: Chain E: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.31 FE.14: 6 residues within 4Å: Chain E: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.64, E:E.108, E:E.144 FE.15: 7 residues within 4Å: Chain E: H.163 Chain K: H.163 Chain Q: H.163 Chain W: H.163 Ligands: FE.33, FE.51, FE.69 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain E, 1 interactions with chain Q, 1 interactions with chain W Metal complexes: K:H.163, E:H.163, Q:H.163, W:H.163 FE.16: 7 residues within 4Å: Chain F: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.31 FE.17: 5 residues within 4Å: Chain F: E.64, E.108, Q.141, E.144 Ligands: FE.16 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 F: H.163 Chain L: H.163 Chain R: H.163 Chain X: H.163 Ligands: FE.36, FE.54, FE.72 No protein-ligand interaction detected (PLIP) FE.19: 8 residues within 4Å: Chain G: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.31 FE.20: 6 residues within 4Å: Chain G: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.19 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.64, G:E.108, G:E.144 FE.21: 5 residues within 4Å: Chain G: H.163 Chain H: H.163 Chain J: H.163, L.167 Chain U: H.163 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:H.163 FE.23: 7 residues within 4Å: Chain H: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.24 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.31 FE.24: 6 residues within 4Å: Chain H: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.23 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.64, H:E.108, H:E.144 FE.26: 7 residues within 4Å: Chain I: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.27 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.31 FE.27: 6 residues within 4Å: Chain I: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.26 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.64, I:E.108, I:E.144 FE.28: 8 residues within 4Å: Chain J: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.31, J:H.67 FE.29: 6 residues within 4Å: Chain J: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.28 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.64, J:E.108, J:E.144 FE.31: 7 residues within 4Å: Chain K: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.32 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.31 FE.32: 6 residues within 4Å: Chain K: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.31 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.64, K:E.108, K:E.144 FE.33: 7 residues within 4Å: Chain E: H.163 Chain K: H.163 Chain Q: H.163 Chain W: H.163 Ligands: FE.15, FE.51, FE.69 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain W, 1 interactions with chain Q, 1 interactions with chain E Metal complexes: K:H.163, W:H.163, Q:H.163, E:H.163 FE.34: 7 residues within 4Å: Chain L: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.35 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.31 FE.35: 5 residues within 4Å: Chain L: E.64, E.108, Q.141, E.144 Ligands: FE.34 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.64, L:E.108, L:E.144 FE.36: 7 residues within 4Å: Chain F: H.163 Chain L: H.163 Chain R: H.163 Chain X: H.163 Ligands: FE.18, FE.54, FE.72 No protein-ligand interaction detected (PLIP) FE.37: 8 residues within 4Å: Chain M: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.38 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.31 FE.38: 6 residues within 4Å: Chain M: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.37 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.64, M:E.108, M:E.144 FE.39: 5 residues within 4Å: Chain I: H.163 Chain M: H.163 Chain N: H.163 Chain P: H.163, L.167 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:H.163 FE.41: 7 residues within 4Å: Chain N: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.42 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.31 FE.42: 6 residues within 4Å: Chain N: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.41 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.64, N:E.108, N:E.144 FE.44: 7 residues within 4Å: Chain O: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.45 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:E.31 FE.45: 6 residues within 4Å: Chain O: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.44 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.64, O:E.108, O:E.144 FE.46: 8 residues within 4Å: Chain P: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.47 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:E.31, P:H.67 FE.47: 6 residues within 4Å: Chain P: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.46 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.64, P:E.108, P:E.144 FE.49: 7 residues within 4Å: Chain Q: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.50 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.31 FE.50: 6 residues within 4Å: Chain Q: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.49 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.64, Q:E.108, Q:E.144 FE.51: 7 residues within 4Å: Chain E: H.163 Chain K: H.163 Chain Q: H.163 Chain W: H.163 Ligands: FE.15, FE.33, FE.69 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain K, 1 interactions with chain W, 1 interactions with chain Q Metal complexes: E:H.163, K:H.163, W:H.163, Q:H.163 FE.52: 7 residues within 4Å: Chain R: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.53 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.31 FE.53: 5 residues within 4Å: Chain R: E.64, E.108, Q.141, E.144 Ligands: FE.52 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.64, R:E.108, R:E.144 FE.54: 7 residues within 4Å: Chain F: H.163 Chain L: H.163 Chain R: H.163 Chain X: H.163 Ligands: FE.18, FE.36, FE.72 No protein-ligand interaction detected (PLIP) FE.55: 8 residues within 4Å: Chain S: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.56 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:E.31 FE.56: 6 residues within 4Å: Chain S: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.55 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.64, S:E.108, S:E.144 FE.57: 5 residues within 4Å: Chain C: H.163 Chain S: H.163 Chain T: H.163 Chain V: H.163, L.167 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:H.163 FE.59: 7 residues within 4Å: Chain T: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.60 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.31 FE.60: 6 residues within 4Å: Chain T: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.59 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.64, T:E.108, T:E.144 FE.62: 7 residues within 4Å: Chain U: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.63 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:E.31 FE.63: 6 residues within 4Å: Chain U: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.62 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.64, U:E.108, U:E.144 FE.64: 8 residues within 4Å: Chain V: E.31, E.64, H.67, I.111, Y.137, Q.141, E.144 Ligands: FE.65 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:E.31, V:H.67 FE.65: 6 residues within 4Å: Chain V: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.64 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.64, V:E.108, V:E.144 FE.67: 7 residues within 4Å: Chain W: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.68 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.31 FE.68: 6 residues within 4Å: Chain W: H.60, E.64, E.108, Q.141, E.144 Ligands: FE.67 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.64, W:E.108, W:E.144 FE.69: 7 residues within 4Å: Chain E: H.163 Chain K: H.163 Chain Q: H.163 Chain W: H.163 Ligands: FE.15, FE.33, FE.51 4 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain W, 1 interactions with chain K, 1 interactions with chain E Metal complexes: Q:H.163, W:H.163, K:H.163, E:H.163 FE.70: 7 residues within 4Å: Chain X: E.31, E.64, H.67, I.111, Q.141, E.144 Ligands: FE.71 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:E.31 FE.71: 5 residues within 4Å: Chain X: E.64, E.108, Q.141, E.144 Ligands: FE.70 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.64, X:E.108, X:E.144 FE.72: 7 residues within 4Å: Chain F: H.163 Chain L: H.163 Chain R: H.163 Chain X: H.163 Ligands: FE.18, FE.36, FE.54 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: M.32, S.35, N.36, Y.65, I.87 Chain F: M.32, Y.65, I.87 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.35, A:S.35, A:N.36 Water bridges: A:Y.65, F:S.35 GOL.7: 8 residues within 4Å: Chain B: M.32, S.35, N.36, Y.65 Chain E: M.32, S.35, N.36, Y.65 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:S.35, E:S.35, B:M.32, B:S.35, B:N.36 Water bridges: E:Y.65, E:Y.65, B:Y.65 GOL.12: 7 residues within 4Å: Chain C: M.32, Y.65, I.87 Chain D: M.32, S.35, N.36, Y.65 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:M.32, D:S.35, D:S.35, D:N.36 Water bridges: C:N.36 GOL.22: 8 residues within 4Å: Chain G: M.32, S.35, N.36, Y.65, I.87 Chain L: M.32, Y.65, I.87 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:S.35, G:S.35, G:N.36 Water bridges: G:Y.65, L:S.35 GOL.25: 8 residues within 4Å: Chain H: M.32, S.35, N.36, Y.65 Chain K: M.32, S.35, N.36, Y.65 8 PLIP interactions: 4 interactions with chain K, 4 interactions with chain H Hydrogen bonds: K:S.35, K:S.35, H:M.32, H:S.35, H:N.36 Water bridges: K:Y.65, K:Y.65, H:Y.65 GOL.30: 7 residues within 4Å: Chain I: M.32, Y.65, I.87 Chain J: M.32, S.35, N.36, Y.65 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:S.35, J:S.35, J:N.36, I:M.32 Water bridges: I:N.36 GOL.40: 8 residues within 4Å: Chain M: M.32, S.35, N.36, Y.65, I.87 Chain R: M.32, Y.65, I.87 5 PLIP interactions: 1 interactions with chain R, 4 interactions with chain M Water bridges: R:S.35, M:Y.65 Hydrogen bonds: M:S.35, M:S.35, M:N.36 GOL.43: 8 residues within 4Å: Chain N: M.32, S.35, N.36, Y.65 Chain Q: M.32, S.35, N.36, Y.65 8 PLIP interactions: 4 interactions with chain Q, 4 interactions with chain N Hydrogen bonds: Q:S.35, Q:S.35, N:M.32, N:S.35, N:N.36 Water bridges: Q:Y.65, Q:Y.65, N:Y.65 GOL.48: 7 residues within 4Å: Chain O: M.32, Y.65, I.87 Chain P: M.32, S.35, N.36, Y.65 5 PLIP interactions: 2 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:M.32, P:S.35, P:S.35, P:N.36 Water bridges: O:N.36 GOL.58: 8 residues within 4Å: Chain S: M.32, S.35, N.36, Y.65, I.87 Chain X: M.32, Y.65, I.87 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain X Hydrogen bonds: S:S.35, S:S.35, S:N.36 Water bridges: S:Y.65, X:S.35 GOL.61: 8 residues within 4Å: Chain T: M.32, S.35, N.36, Y.65 Chain W: M.32, S.35, N.36, Y.65 8 PLIP interactions: 4 interactions with chain W, 4 interactions with chain T Hydrogen bonds: W:S.35, W:S.35, T:M.32, T:S.35, T:N.36 Water bridges: W:Y.65, W:Y.65, T:Y.65 GOL.66: 7 residues within 4Å: Chain U: M.32, Y.65, I.87 Chain V: M.32, S.35, N.36, Y.65 5 PLIP interactions: 2 interactions with chain U, 3 interactions with chain V Hydrogen bonds: U:M.32, V:S.35, V:S.35, V:N.36 Water bridges: U:N.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, K.J. et al., The crystal structure of ferritin from Helicobacter pylori reveals unusual conformational changes for iron uptake. J.Mol.Biol. (2009)

Release Date

2009-07-28

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