SMTL ID : 3wnw.1

Structure of Mouse H-chain modified ferritin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-24-mer

Ligands

40 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.45, A:E.80, A:H.83, H2O.4, H2O.4 MG.2: 1 residues within 4Å: Chain B: E.152 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: E.45, E.80, H.83 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.45, B:E.80, B:H.83, H2O.8, H2O.10 MG.9: 4 residues within 4Å: Chain A: D.149, E.152 Chain C: D.149, E.152 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.152, H2O.5, H2O.5, H2O.9, H2O.9 MG.10: 4 residues within 4Å: Chain C: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.45, C:E.80, C:H.83, H2O.11, H2O.12 MG.15: 4 residues within 4Å: Chain D: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.45, D:E.80, D:H.83, H2O.17, H2O.17 MG.16: 3 residues within 4Å: Chain D: E.152 Chain E: E.152 Chain F: E.152 No protein-ligand interaction detected (PLIP) MG.19: 6 residues within 4Å: Chain D: D.149, E.152 Chain E: D.149, E.152 Chain F: D.149, E.152 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.149, H2O.17, H2O.19, H2O.23, H2O.23 MG.20: 4 residues within 4Å: Chain E: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.45, E:E.80, E:H.83, H2O.21, H2O.22 MG.23: 4 residues within 4Å: Chain F: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.45, F:E.80, F:H.83, H2O.27, H2O.27 MG.24: 4 residues within 4Å: Chain G: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.45, G:E.80, G:H.83, H2O.32, H2O.33 MG.25: 2 residues within 4Å: Chain G: E.152 Chain H: E.152 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain H: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.45, H:E.80, H:H.83, H2O.33, H2O.36 MG.28: 6 residues within 4Å: Chain G: D.149, E.152 Chain H: D.149, E.152 Chain I: D.149, E.152 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: H:D.149, I:E.152, H2O.31, H2O.34, H2O.37 MG.29: 4 residues within 4Å: Chain I: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.45, I:E.80, I:H.83, H2O.38, H2O.41 MG.30: 4 residues within 4Å: Chain J: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.45, J:E.80, J:H.83, H2O.42, H2O.45 MG.31: 2 residues within 4Å: Chain J: E.152 Chain L: E.152 No protein-ligand interaction detected (PLIP) MG.32: 6 residues within 4Å: Chain J: D.149, E.152 Chain K: D.149, E.152 Chain L: D.149, E.152 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: L:E.152, K:D.149, H2O.45, H2O.50, H2O.50 MG.33: 4 residues within 4Å: Chain K: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.45, K:E.80, K:H.83, H2O.47, H2O.49 MG.36: 4 residues within 4Å: Chain L: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.45, L:E.80, L:H.83, H2O.51, H2O.51 MG.39: 4 residues within 4Å: Chain M: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.45, M:E.80, M:H.83, H2O.56, H2O.57 MG.40: 1 residues within 4Å: Chain N: E.152 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain N: E.45, E.80, H.83 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.45, N:E.80, N:H.83, H2O.61, H2O.62 MG.47: 4 residues within 4Å: Chain M: D.149, E.152 Chain O: D.149, E.152 5 PLIP interactions: 1 interactions with chain M, 4 Ligand-Water interactions Metal complexes: M:E.152, H2O.57, H2O.58, H2O.62, H2O.62 MG.48: 4 residues within 4Å: Chain O: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.45, O:E.80, O:H.83, H2O.64, H2O.64 MG.53: 4 residues within 4Å: Chain P: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.45, P:E.80, P:H.83, H2O.70, H2O.70 MG.54: 3 residues within 4Å: Chain P: E.152 Chain Q: E.152 Chain R: E.152 No protein-ligand interaction detected (PLIP) MG.57: 6 residues within 4Å: Chain P: D.149, E.152 Chain Q: D.149, E.152 Chain R: D.149, E.152 5 PLIP interactions: 1 interactions with chain Q, 4 Ligand-Water interactions Metal complexes: Q:D.149, H2O.70, H2O.72, H2O.76, H2O.76 MG.58: 4 residues within 4Å: Chain Q: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.45, Q:E.80, Q:H.83, H2O.74, H2O.74 MG.61: 4 residues within 4Å: Chain R: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.45, R:E.80, R:H.83, H2O.79, H2O.80 MG.62: 4 residues within 4Å: Chain S: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.45, S:E.80, S:H.83, H2O.84, H2O.85 MG.63: 2 residues within 4Å: Chain S: E.152 Chain T: E.152 No protein-ligand interaction detected (PLIP) MG.64: 4 residues within 4Å: Chain T: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.45, T:E.80, T:H.83, H2O.86, H2O.88 MG.66: 6 residues within 4Å: Chain S: D.149, E.152 Chain T: D.149, E.152 Chain U: D.149, E.152 5 PLIP interactions: 1 interactions with chain T, 1 interactions with chain U, 3 Ligand-Water interactions Metal complexes: T:D.149, U:E.152, H2O.84, H2O.87, H2O.90 MG.67: 4 residues within 4Å: Chain U: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.45, U:E.80, U:H.83, H2O.90, H2O.94 MG.68: 4 residues within 4Å: Chain V: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.45, V:E.80, V:H.83, H2O.95, H2O.98 MG.69: 2 residues within 4Å: Chain V: E.152 Chain X: E.152 No protein-ligand interaction detected (PLIP) MG.70: 6 residues within 4Å: Chain V: D.149, E.152 Chain W: D.149, E.152 Chain X: D.149, E.152 5 PLIP interactions: 1 interactions with chain W, 1 interactions with chain X, 3 Ligand-Water interactions Metal complexes: W:D.149, X:E.152, H2O.98, H2O.103, H2O.103 MG.71: 4 residues within 4Å: Chain W: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.45, W:E.80, W:H.83, H2O.100, H2O.102 MG.74: 4 residues within 4Å: Chain X: E.45, E.80, H.83, Q.159 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.45, X:E.80, X:H.83, H2O.104, H2O.104

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

FE.3: 7 residues within 4Å: Chain A: L.187, H.191 Chain J: H.191 Chain P: L.187, H.191 Chain S: L.187, H.191 No protein-ligand interaction detected (PLIP) FE.7: 9 residues within 4Å: Chain B: L.187, H.191 Chain F: L.187, H.191 Chain N: L.187, H.191 Chain R: L.187, H.191 Ligands: FE.45 No protein-ligand interaction detected (PLIP) FE.11: 7 residues within 4Å: Chain C: L.187, H.191 Chain E: L.187, H.191 Chain I: H.191 Chain K: L.187, H.191 No protein-ligand interaction detected (PLIP) FE.27: 9 residues within 4Å: Chain H: L.187, H.191 Chain L: L.187, H.191 Chain T: L.187, H.191 Chain X: L.187, H.191 Ligands: FE.65 No protein-ligand interaction detected (PLIP) FE.41: 7 residues within 4Å: Chain D: L.187, H.191 Chain G: L.187, H.191 Chain M: L.187, H.191 Chain V: H.191 No protein-ligand interaction detected (PLIP) FE.45: 9 residues within 4Å: Chain B: L.187, H.191 Chain F: L.187, H.191 Chain N: L.187, H.191 Chain R: L.187, H.191 Ligands: FE.7 No protein-ligand interaction detected (PLIP) FE.49: 7 residues within 4Å: Chain O: L.187, H.191 Chain Q: L.187, H.191 Chain U: H.191 Chain W: L.187, H.191 No protein-ligand interaction detected (PLIP) FE.65: 9 residues within 4Å: Chain H: L.187, H.191 Chain L: L.187, H.191 Chain T: L.187, H.191 Chain X: L.187, H.191 Ligands: FE.27 No protein-ligand interaction detected (PLIP)

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.56, C.57, D.60 Chain R: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: E.85, M.88, K.89 Chain R: L.53, S.56, D.60, L.74 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain C: E.85, M.88, K.89 Chain J: S.56, D.60 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain C: S.56, C.57, D.60 Chain J: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain D: S.56, C.57, D.60 Chain I: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain D: E.85 Chain I: S.56, D.60, A.70 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: S.56, C.57, D.60 Chain E: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: E.85 Chain E: S.56, C.57, D.60, A.70 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain H: E.85, M.88, K.89 Chain K: S.56, D.60 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain H: S.56, C.57, D.60 Chain K: E.85, M.88, K.89 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain L: S.56, C.57, D.60, L.74 Chain S: E.85 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain L: E.85, M.88, K.89 Chain S: S.56, C.57, D.60 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain F: E.85, M.88, K.89, N.92 Chain M: S.56, C.57, D.60 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain F: L.53, S.56, D.60, L.74 Chain M: E.85, M.88, K.89 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain O: E.85, M.88, K.89 Chain V: S.56, D.60 Ligand excluded by PLIP GOL.51: 7 residues within 4Å: Chain O: S.56, C.57, D.60 Chain V: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.55: 7 residues within 4Å: Chain P: S.56, C.57, D.60 Chain U: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain P: E.85 Chain U: S.56, D.60, A.70 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain N: S.56, C.57, D.60 Chain Q: E.85, M.88, K.89, N.92 Ligand excluded by PLIP GOL.60: 5 residues within 4Å: Chain N: E.85 Chain Q: S.56, C.57, D.60, A.70 Ligand excluded by PLIP GOL.72: 5 residues within 4Å: Chain T: E.85, M.88, K.89 Chain W: S.56, D.60 Ligand excluded by PLIP GOL.73: 6 residues within 4Å: Chain T: S.56, C.57, D.60 Chain W: E.85, M.88, K.89 Ligand excluded by PLIP GOL.75: 5 residues within 4Å: Chain G: E.85 Chain X: S.56, C.57, D.60, L.74 Ligand excluded by PLIP GOL.76: 6 residues within 4Å: Chain G: S.56, C.57, D.60 Chain X: E.85, M.88, K.89 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain B: N.29, Y.30, H.31, K.142, D.144 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.29, H2O.6, H2O.7 K.14: 2 residues within 4Å: Chain C: Y.58, D.110 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.58, H2O.11 K.46: 5 residues within 4Å: Chain N: N.29, Y.30, H.31, K.142, D.144 3 PLIP interactions: 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:N.29, H2O.59, H2O.59 K.52: 2 residues within 4Å: Chain O: Y.58, D.110 2 PLIP interactions: 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:Y.58, H2O.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarivach, R. et al., Studies of ferritin-M6A. To be Published

Release Date

2015-01-28

Peptides

Ferritin heavy chain: 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
A

N
B

O
C

P
D

Q
E

R
F

S
G

T
H

U
I

V
J

W
K

X
L

Ferritin heavy chain