SMTL ID : 8y6f.1

The crystal structure of MMPs cleavable human heavy chain ferritin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-24-mer

Ligands

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: R.17, Q.18, N.19, Y.20 Ligand excluded by PLIP CL.2: 8 residues within 4Å: Chain A: L.184, H.188 Chain B: L.184, H.188 Chain C: L.184, H.188 Chain D: L.184, H.188 Ligand excluded by PLIP CL.11: 9 residues within 4Å: Chain E: L.184, H.188 Chain I: L.184, H.188 Chain Q: L.184, H.188 Chain U: L.184, H.188 Ligands: CL.36 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain L: F.140, H.144 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain M: R.17, Q.18, N.19, Y.20 Ligand excluded by PLIP CL.27: 8 residues within 4Å: Chain M: L.184, H.188 Chain N: L.184, H.188 Chain O: L.184, H.188 Chain P: L.184, H.188 Ligand excluded by PLIP CL.36: 9 residues within 4Å: Chain E: L.184, H.188 Chain I: L.184, H.188 Chain Q: L.184, H.188 Chain U: L.184, H.188 Ligands: CL.11 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain X: F.140, H.144 Ligand excluded by PLIP

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

FE.3: 3 residues within 4Å: Chain A: E.35, E.70, H.73 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.35, A:E.70, A:H.73, H2O.2 FE.4: 6 residues within 4Å: Chain B: D.139, E.142 Chain G: D.139, E.142 Chain L: D.139, E.142 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain G, 2 interactions with chain B Metal complexes: L:D.139, L:E.142, G:D.139, B:D.139, B:E.142 FE.5: 3 residues within 4Å: Chain B: E.35, E.70, H.73 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.35, B:E.70, B:H.73, H2O.12 FE.7: 3 residues within 4Å: Chain C: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.35, C:E.70, C:H.73, H2O.17, H2O.19 FE.9: 7 residues within 4Å: Chain D: D.139, E.142 Chain T: D.139, E.142 Chain V: D.139, E.142 Ligands: FE.40 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain T, 2 interactions with chain V Metal complexes: D:E.142, T:E.142, V:D.139, V:E.142 FE.10: 4 residues within 4Å: Chain D: E.35, E.70, H.73, Q.149 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.35, D:E.70, D:H.73, H2O.25 FE.12: 4 residues within 4Å: Chain E: E.35, E.70, H.73, Q.149 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.35, E:E.70, E:H.73, H2O.33, H2O.33 FE.13: 3 residues within 4Å: Chain F: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.35, F:E.70, F:H.73, H2O.40, H2O.41 FE.14: 3 residues within 4Å: Chain G: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.35, G:E.70, G:H.73, H2O.48, H2O.49 FE.15: 6 residues within 4Å: Chain H: D.139, E.142 Chain J: D.139 Chain P: D.139, E.142 Ligands: FE.34 4 PLIP interactions: 2 interactions with chain P, 1 interactions with chain J, 1 interactions with chain H Metal complexes: P:D.139, P:E.142, J:D.139, H:E.142 FE.16: 3 residues within 4Å: Chain H: E.35, E.70, H.73 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.35, H:E.70, H:H.73, H2O.58 FE.17: 6 residues within 4Å: Chain C: D.139, T.143 Chain I: D.139, T.143 Chain R: D.139 Ligands: NA.6 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: I:D.139, C:D.139, H2O.141, H2O.142 FE.18: 4 residues within 4Å: Chain I: E.35, E.70, H.73, Q.149 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.35, I:E.70, I:H.73, H2O.65, H2O.67 FE.20: 3 residues within 4Å: Chain J: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.35, J:E.70, J:H.73, H2O.73, H2O.74 FE.21: 6 residues within 4Å: Chain A: D.139, E.142 Chain E: D.139, E.142 Chain K: D.139, E.142 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain K, 1 interactions with chain A Metal complexes: E:D.139, E:E.142, K:D.139, K:E.142, A:E.142 FE.22: 4 residues within 4Å: Chain K: E.35, E.70, H.73, Q.149 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.35, K:E.70, K:H.73, H2O.82 FE.25: 4 residues within 4Å: Chain L: E.35, E.70, H.73, Q.149 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.35, L:E.70, L:H.73, H2O.90, H2O.93 FE.28: 3 residues within 4Å: Chain M: E.35, E.70, H.73 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.35, M:E.70, M:H.73, H2O.98 FE.29: 6 residues within 4Å: Chain N: D.139, E.142 Chain S: D.139, E.142 Chain X: D.139, E.142 5 PLIP interactions: 2 interactions with chain X, 2 interactions with chain N, 1 interactions with chain S Metal complexes: X:D.139, X:E.142, N:D.139, N:E.142, S:D.139 FE.30: 3 residues within 4Å: Chain N: E.35, E.70, H.73 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.35, N:E.70, N:H.73, H2O.109 FE.32: 3 residues within 4Å: Chain O: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.35, O:E.70, O:H.73, H2O.114, H2O.116 FE.34: 7 residues within 4Å: Chain H: D.139, E.142 Chain J: D.139, E.142 Chain P: D.139, E.142 Ligands: FE.15 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain H, 1 interactions with chain P Metal complexes: J:D.139, J:E.142, H:E.142, P:E.142 FE.35: 4 residues within 4Å: Chain P: E.35, E.70, H.73, Q.149 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.35, P:E.70, P:H.73, H2O.122 FE.37: 4 residues within 4Å: Chain Q: E.35, E.70, H.73, Q.149 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.35, Q:E.70, Q:H.73, H2O.130, H2O.130 FE.38: 3 residues within 4Å: Chain R: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.35, R:E.70, R:H.73, H2O.137, H2O.138 FE.39: 3 residues within 4Å: Chain S: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.35, S:E.70, S:H.73, H2O.145, H2O.146 FE.40: 6 residues within 4Å: Chain D: D.139, E.142 Chain T: D.139, E.142 Chain V: D.139 Ligands: FE.9 4 PLIP interactions: 1 interactions with chain T, 2 interactions with chain D, 1 interactions with chain V Metal complexes: T:E.142, D:D.139, D:E.142, V:D.139 FE.41: 3 residues within 4Å: Chain T: E.35, E.70, H.73 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.35, T:E.70, T:H.73, H2O.155 FE.42: 6 residues within 4Å: Chain F: D.139 Chain O: D.139, T.143 Chain U: D.139, T.143 Ligands: NA.31 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: U:D.139, O:D.139, H2O.44, H2O.45 FE.43: 4 residues within 4Å: Chain U: E.35, E.70, H.73, Q.149 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.35, U:E.70, U:H.73, H2O.162, H2O.164 FE.45: 3 residues within 4Å: Chain V: E.35, E.70, H.73 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.35, V:E.70, V:H.73, H2O.170, H2O.171 FE.46: 6 residues within 4Å: Chain M: D.139, E.142 Chain Q: D.139, E.142 Chain W: D.139, E.142 5 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain W, 1 interactions with chain M Metal complexes: Q:D.139, Q:E.142, W:D.139, W:E.142, M:E.142 FE.47: 4 residues within 4Å: Chain W: E.35, E.70, H.73, Q.149 4 PLIP interactions: 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.35, W:E.70, W:H.73, H2O.179 FE.50: 4 residues within 4Å: Chain X: E.35, E.70, H.73, Q.149 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.35, X:E.70, X:H.73, H2O.187, H2O.190

8 x NA: SODIUM ION(Non-functional Binders)

NA.6: 7 residues within 4Å: Chain C: D.139, E.142 Chain I: D.139, E.142 Chain R: D.139, E.142 Ligands: FE.17 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.139, I:D.139 NA.8: 3 residues within 4Å: Chain D: Q.66, E.70, E.115 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.115 Water bridges: D:Q.149 NA.19: 8 residues within 4Å: Chain F: L.184, H.188 Chain G: L.184, H.188 Chain J: L.184, H.188 Chain K: L.184, H.188 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.188 NA.24: 2 residues within 4Å: Chain L: E.70, E.115 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Q.66 Water bridges: L:Q.149 NA.31: 7 residues within 4Å: Chain F: D.139, E.142 Chain O: D.139, E.142 Chain U: D.139, E.142 Ligands: FE.42 3 PLIP interactions: 2 interactions with chain O, 1 interactions with chain F Hydrogen bonds: O:D.139, O:E.142, F:D.139 NA.33: 3 residues within 4Å: Chain P: Q.66, E.70, E.115 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:E.70 Water bridges: P:Q.149 NA.44: 8 residues within 4Å: Chain R: L.184, H.188 Chain S: L.184, H.188 Chain V: L.184, H.188 Chain W: L.184, H.188 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:H.188 NA.49: 2 residues within 4Å: Chain X: E.70, E.115 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:E.115 Water bridges: X:Q.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, W. et al., Engineered protein cages with enhanced extracellular drug release for elevated antitumor efficacy. Int.J.Biol.Macromol. (2024)

Release Date

2024-07-17

Peptides

Ferritin: 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