SMTL ID : 6kh0.1

Design and crystal structure of protein MOFs with ferritin nanocages as linkers and nickel clusters as nodes

Coordinates

PDB Format

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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.23, A:E.58, A:H.61, H2O.4 FE.2: 4 residues within 4Å: Chain B: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.23, B:E.58, B:H.61, H2O.16 FE.3: 4 residues within 4Å: Chain C: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.23, C:E.58, C:H.61, H2O.29 FE.4: 5 residues within 4Å: Chain D: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.23, D:E.58, D:E.58, D:H.61, H2O.39 FE.5: 4 residues within 4Å: Chain E: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.23, E:E.58, H2O.48 FE.6: 4 residues within 4Å: Chain F: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.23, F:E.58, H2O.58 FE.7: 4 residues within 4Å: Chain G: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.23, G:E.58, G:H.61, H2O.72 FE.8: 4 residues within 4Å: Chain H: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.23, H:E.58, H:H.61, H2O.84 FE.9: 4 residues within 4Å: Chain I: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.23, I:E.58, I:H.61, H2O.97 FE.10: 5 residues within 4Å: Chain J: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.23, J:E.58, J:E.58, J:H.61, H2O.107 FE.11: 4 residues within 4Å: Chain K: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.23, K:E.58, H2O.116 FE.12: 4 residues within 4Å: Chain L: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.23, L:E.58, H2O.127 FE.13: 4 residues within 4Å: Chain M: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.23, M:E.58, M:H.61, H2O.140 FE.14: 4 residues within 4Å: Chain N: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.23, N:E.58, N:H.61, H2O.152 FE.15: 4 residues within 4Å: Chain O: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.23, O:E.58, O:H.61, H2O.165 FE.16: 5 residues within 4Å: Chain P: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.23, P:E.58, P:E.58, P:H.61, H2O.175 FE.17: 4 residues within 4Å: Chain Q: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.23, Q:E.58, H2O.185 FE.18: 4 residues within 4Å: Chain R: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.23, R:E.58, H2O.195 FE.19: 4 residues within 4Å: Chain S: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.23, S:E.58, S:H.61, H2O.208 FE.20: 4 residues within 4Å: Chain T: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.23, T:E.58, T:H.61, H2O.220 FE.21: 4 residues within 4Å: Chain U: E.23, E.58, H.61, V.106 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.23, U:E.58, U:H.61, H2O.233 FE.22: 5 residues within 4Å: Chain V: E.23, E.58, H.61, V.106, Q.137 5 PLIP interactions: 4 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.23, V:E.58, V:E.58, V:H.61, H2O.243 FE.23: 4 residues within 4Å: Chain W: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.23, W:E.58, H2O.253 FE.24: 4 residues within 4Å: Chain X: E.23, E.58, H.61, V.106 3 PLIP interactions: 2 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.23, X:E.58, H2O.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, C. et al., Structural Insight into Binary Protein Metal-Organic Frameworks with Ferritin Nanocages as Linkers and Nickel Clusters as Nodes. Chemistry (2020)

Release Date

2020-01-29

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

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