SMTL ID : 7urh.1

Crystal structure of Ferritin 2 from Caenorhabditis elegans, FTN-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.22, A:E.57, A:H.60, H2O.1, H2O.6 FE.2: 4 residues within 4Å: Chain B: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.22, B:E.57, B:H.60, H2O.9, H2O.15 FE.4: 4 residues within 4Å: Chain C: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.22, C:E.57, C:H.60, H2O.19, H2O.25 FE.6: 4 residues within 4Å: Chain D: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.22, D:E.57, D:H.60, H2O.28, H2O.33 FE.8: 4 residues within 4Å: Chain E: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.22, E:E.57, E:H.60, H2O.37, H2O.42 FE.9: 4 residues within 4Å: Chain F: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.22, F:E.57, F:H.60, H2O.46, H2O.51 FE.10: 4 residues within 4Å: Chain G: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.22, G:E.57, G:H.60, H2O.55, H2O.60 FE.11: 4 residues within 4Å: Chain H: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.22, H:E.57, H:H.60, H2O.64, H2O.69 FE.13: 4 residues within 4Å: Chain I: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.22, I:E.57, I:H.60, H2O.73, H2O.79 FE.15: 4 residues within 4Å: Chain J: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.22, J:E.57, J:H.60, H2O.82, H2O.87 FE.17: 4 residues within 4Å: Chain K: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.22, K:E.57, K:H.60, H2O.91, H2O.96 FE.18: 4 residues within 4Å: Chain L: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.22, L:E.57, L:H.60, H2O.100, H2O.106 FE.19: 4 residues within 4Å: Chain M: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.22, M:E.57, M:H.60, H2O.109, H2O.114 FE.20: 4 residues within 4Å: Chain N: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.22, N:E.57, N:H.60, H2O.118, H2O.123 FE.22: 4 residues within 4Å: Chain O: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.22, O:E.57, O:H.60, H2O.127, H2O.133 FE.24: 4 residues within 4Å: Chain P: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.22, P:E.57, P:H.60, H2O.136, H2O.142 FE.26: 4 residues within 4Å: Chain Q: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.22, Q:E.57, Q:H.60, H2O.145, H2O.150 FE.27: 4 residues within 4Å: Chain R: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.22, R:E.57, R:H.60, H2O.154, H2O.160 FE.28: 4 residues within 4Å: Chain S: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.22, S:E.57, S:H.60, H2O.163, H2O.168 FE.29: 4 residues within 4Å: Chain T: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.22, T:E.57, T:H.60, H2O.172, H2O.177 FE.31: 4 residues within 4Å: Chain U: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.22, U:E.57, U:H.60, H2O.181, H2O.187 FE.33: 4 residues within 4Å: Chain V: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.22, V:E.57, V:H.60, H2O.190, H2O.196 FE.35: 4 residues within 4Å: Chain W: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.22, W:E.57, W:H.60, H2O.199, H2O.204 FE.36: 4 residues within 4Å: Chain X: E.22, E.57, H.60, N.105 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.22, X:E.57, X:H.60, H2O.208, H2O.214

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: L.23, S.26, Y.27, L.30, R.58 Chain B: L.23, S.26, R.58, I.80 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.27, A:Y.27, A:L.30, B:I.80 Hydrogen bonds: A:S.26, A:S.26 MPD.5: 8 residues within 4Å: Chain C: L.23, S.26, Y.27, R.58 Chain E: L.23, S.26, Y.27, R.58 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:L.23, C:Y.27, E:Y.27 Hydrogen bonds: C:S.26, E:S.26, E:S.26 MPD.7: 9 residues within 4Å: Chain D: L.23, S.26, Y.27, R.58 Chain F: L.23, S.26, Y.27, R.58, I.80 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:Y.27, F:I.80, D:Y.27 Hydrogen bonds: F:S.26 MPD.12: 9 residues within 4Å: Chain G: L.23, S.26, Y.27, L.30, R.58 Chain H: L.23, S.26, R.58, I.80 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: H:I.80, G:Y.27, G:Y.27, G:L.30 Hydrogen bonds: G:S.26, G:S.26 MPD.14: 8 residues within 4Å: Chain I: L.23, S.26, Y.27, R.58 Chain K: L.23, S.26, Y.27, R.58 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain K Hydrophobic interactions: I:L.23, I:Y.27, K:Y.27 Hydrogen bonds: I:S.26, K:S.26, K:S.26 MPD.16: 9 residues within 4Å: Chain J: L.23, S.26, Y.27, R.58 Chain L: L.23, S.26, Y.27, R.58, I.80 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain J Hydrophobic interactions: L:Y.27, L:I.80, J:Y.27 Hydrogen bonds: L:S.26 MPD.21: 9 residues within 4Å: Chain M: L.23, S.26, Y.27, L.30, R.58 Chain N: L.23, S.26, R.58, I.80 6 PLIP interactions: 1 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:I.80, M:Y.27, M:Y.27, M:L.30 Hydrogen bonds: M:S.26, M:S.26 MPD.23: 8 residues within 4Å: Chain O: L.23, S.26, Y.27, R.58 Chain Q: L.23, S.26, Y.27, R.58 6 PLIP interactions: 3 interactions with chain O, 3 interactions with chain Q Hydrophobic interactions: O:L.23, O:Y.27, Q:Y.27 Hydrogen bonds: O:S.26, Q:S.26, Q:S.26 MPD.25: 9 residues within 4Å: Chain P: L.23, S.26, Y.27, R.58 Chain R: L.23, S.26, Y.27, R.58, I.80 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain P Hydrophobic interactions: R:Y.27, R:I.80, P:Y.27 Hydrogen bonds: R:S.26 MPD.30: 9 residues within 4Å: Chain S: L.23, S.26, Y.27, L.30, R.58 Chain T: L.23, S.26, R.58, I.80 6 PLIP interactions: 5 interactions with chain S, 1 interactions with chain T Hydrophobic interactions: S:Y.27, S:Y.27, S:L.30, T:I.80 Hydrogen bonds: S:S.26, S:S.26 MPD.32: 8 residues within 4Å: Chain U: L.23, S.26, Y.27, R.58 Chain W: L.23, S.26, Y.27, R.58 6 PLIP interactions: 3 interactions with chain W, 3 interactions with chain U Hydrophobic interactions: W:Y.27, U:L.23, U:Y.27 Hydrogen bonds: W:S.26, W:S.26, U:S.26 MPD.34: 9 residues within 4Å: Chain V: L.23, S.26, Y.27, R.58 Chain X: L.23, S.26, Y.27, R.58, I.80 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain V Hydrophobic interactions: X:Y.27, X:I.80, V:Y.27 Hydrogen bonds: X:S.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mubarak, S.S.M. et al., Biochemical Characterization of Caenorhabditis elegans Ferritins. Biochemistry (2023)

Release Date

2023-04-26

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
I

F
K

G
A

H
C

I
E

J
G

K
I

L
K

M
A

N
C

O
E

P
G

Q
I

R
K

S
A

T
C

U
E

V
G

W
I

X
K

Ferritin

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