SMTL ID : 8pp5.1

Unitary crystal structure of positively supercharged ferritin variant Ftn(pos)-m1 (Mg Formate condition)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.23, A:E.58, A:H.61, H2O.1, H2O.1 FE.3: 4 residues within 4Å: Chain B: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.23, B:E.58, B:H.61, H2O.7, H2O.7 FE.5: 5 residues within 4Å: Chain C: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.58, C:H.61, H2O.13, H2O.13 FE.8: 4 residues within 4Å: Chain D: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.23, D:E.58, D:H.61, H2O.18, H2O.19 FE.9: 4 residues within 4Å: Chain E: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.23, E:E.58, E:H.61, H2O.25, H2O.27 FE.10: 4 residues within 4Å: Chain F: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.23, F:E.58, F:H.61, H2O.30, H2O.31 FE.11: 4 residues within 4Å: Chain G: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.23, G:E.58, G:H.61, H2O.36, H2O.36 FE.13: 4 residues within 4Å: Chain H: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.23, H:E.58, H:H.61, H2O.42, H2O.42 FE.15: 5 residues within 4Å: Chain I: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.23, I:E.58, I:H.61, H2O.48, H2O.48 FE.18: 4 residues within 4Å: Chain J: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.23, J:E.58, J:H.61, H2O.54, H2O.54 FE.19: 4 residues within 4Å: Chain K: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.23, K:E.58, K:H.61, H2O.61, H2O.62 FE.20: 4 residues within 4Å: Chain L: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.23, L:E.58, L:H.61, H2O.65, H2O.66 FE.21: 4 residues within 4Å: Chain M: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.23, M:E.58, M:H.61, H2O.71, H2O.72 FE.23: 4 residues within 4Å: Chain N: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.23, N:E.58, N:H.61, H2O.77, H2O.77 FE.25: 5 residues within 4Å: Chain O: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.23, O:E.58, O:H.61, H2O.83, H2O.84 FE.28: 4 residues within 4Å: Chain P: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.23, P:E.58, P:H.61, H2O.89, H2O.89 FE.29: 4 residues within 4Å: Chain Q: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.23, Q:E.58, Q:H.61, H2O.96, H2O.97 FE.30: 4 residues within 4Å: Chain R: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.23, R:E.58, R:H.61, H2O.101, H2O.101 FE.31: 4 residues within 4Å: Chain S: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.23, S:E.58, S:H.61, H2O.106, H2O.107 FE.33: 4 residues within 4Å: Chain T: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.23, T:E.58, T:H.61, H2O.112, H2O.113 FE.35: 5 residues within 4Å: Chain U: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.23, U:E.58, U:H.61, H2O.119, H2O.119 FE.38: 4 residues within 4Å: Chain V: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.23, V:E.58, V:H.61, H2O.124, H2O.124 FE.39: 4 residues within 4Å: Chain W: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.23, W:E.58, W:H.61, H2O.131, H2O.132 FE.40: 4 residues within 4Å: Chain X: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.23, X:E.58, X:H.61, H2O.136, H2O.136

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.130 Chain B: E.130 Chain D: E.130 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain A: D.127, E.130 Chain B: D.127, E.130 Chain D: D.127, E.130 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain C: D.127, T.131 Chain E: D.127, T.131 Chain F: D.127, T.131 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: E.130 Chain E: E.130 Chain F: E.130 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain G: E.130 Chain H: E.130 Chain J: E.130 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain G: D.127, E.130 Chain H: D.127, E.130 Chain J: D.127, E.130 No protein-ligand interaction detected (PLIP) MG.16: 6 residues within 4Å: Chain I: D.127, T.131 Chain K: D.127, T.131 Chain L: D.127, T.131 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain I: E.130 Chain K: E.130 Chain L: E.130 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain M: E.130 Chain N: E.130 Chain P: E.130 No protein-ligand interaction detected (PLIP) MG.24: 6 residues within 4Å: Chain M: D.127, E.130 Chain N: D.127, E.130 Chain P: D.127, E.130 No protein-ligand interaction detected (PLIP) MG.26: 6 residues within 4Å: Chain O: D.127, T.131 Chain Q: D.127, T.131 Chain R: D.127, T.131 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain O: E.130 Chain Q: E.130 Chain R: E.130 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain S: E.130 Chain T: E.130 Chain V: E.130 No protein-ligand interaction detected (PLIP) MG.34: 6 residues within 4Å: Chain S: D.127, E.130 Chain T: D.127, E.130 Chain V: D.127, E.130 No protein-ligand interaction detected (PLIP) MG.36: 6 residues within 4Å: Chain U: D.127, T.131 Chain W: D.127, T.131 Chain X: D.127, T.131 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain U: E.130 Chain W: E.130 Chain X: E.130 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, L. et al., Assembly Requirements for the Construction of Large-Scale Binary Protein Structures. Biomacromolecules (2024)

Release Date

2023-12-27

Peptides

Ferritin heavy chain, N-terminally processed: 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 heavy chain, N-terminally processed