SMTL ID : 6kh3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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.5, H2O.5 FE.5: 4 residues within 4Å: Chain C: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.58, C:H.61, H2O.9, H2O.10 FE.7: 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.14, H2O.14 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.18, H2O.19 FE.11: 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.22, H2O.23 FE.13: 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.27, H2O.27 FE.15: 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.31, H2O.32 FE.17: 4 residues within 4Å: Chain I: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.23, I:E.58, I:H.61, H2O.36, H2O.36 FE.19: 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.40, H2O.41 FE.21: 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.44, H2O.45 FE.23: 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.49, H2O.49 FE.25: 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.53, H2O.54 FE.27: 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.58, H2O.58 FE.29: 4 residues within 4Å: Chain O: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.23, O:E.58, O:H.61, H2O.62, H2O.62 FE.31: 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.66, H2O.67 FE.33: 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.71, H2O.71 FE.35: 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.75, H2O.76 FE.37: 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.79, H2O.80 FE.39: 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.84, H2O.84 FE.41: 4 residues within 4Å: Chain U: E.23, E.58, H.61, V.106 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.23, U:E.58, U:H.61, H2O.88, H2O.89 FE.43: 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.93, H2O.93 FE.45: 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.97, H2O.98 FE.47: 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.101, H2O.102

24 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 2 residues within 4Å: Chain A: T.91, H.157 Ligand excluded by PLIP NI.4: 2 residues within 4Å: Chain B: T.91, H.157 Ligand excluded by PLIP NI.6: 2 residues within 4Å: Chain C: T.91, H.157 Ligand excluded by PLIP NI.8: 2 residues within 4Å: Chain D: T.91, H.157 Ligand excluded by PLIP NI.10: 2 residues within 4Å: Chain E: T.91, H.157 Ligand excluded by PLIP NI.12: 2 residues within 4Å: Chain F: T.91, H.157 Ligand excluded by PLIP NI.14: 2 residues within 4Å: Chain G: T.91, H.157 Ligand excluded by PLIP NI.16: 2 residues within 4Å: Chain H: T.91, H.157 Ligand excluded by PLIP NI.18: 2 residues within 4Å: Chain I: T.91, H.157 Ligand excluded by PLIP NI.20: 2 residues within 4Å: Chain J: T.91, H.157 Ligand excluded by PLIP NI.22: 2 residues within 4Å: Chain K: T.91, H.157 Ligand excluded by PLIP NI.24: 2 residues within 4Å: Chain L: T.91, H.157 Ligand excluded by PLIP NI.26: 2 residues within 4Å: Chain M: T.91, H.157 Ligand excluded by PLIP NI.28: 2 residues within 4Å: Chain N: T.91, H.157 Ligand excluded by PLIP NI.30: 2 residues within 4Å: Chain O: T.91, H.157 Ligand excluded by PLIP NI.32: 2 residues within 4Å: Chain P: T.91, H.157 Ligand excluded by PLIP NI.34: 2 residues within 4Å: Chain Q: T.91, H.157 Ligand excluded by PLIP NI.36: 2 residues within 4Å: Chain R: T.91, H.157 Ligand excluded by PLIP NI.38: 2 residues within 4Å: Chain S: T.91, H.157 Ligand excluded by PLIP NI.40: 2 residues within 4Å: Chain T: T.91, H.157 Ligand excluded by PLIP NI.42: 2 residues within 4Å: Chain U: T.91, H.157 Ligand excluded by PLIP NI.44: 2 residues within 4Å: Chain V: T.91, H.157 Ligand excluded by PLIP NI.46: 2 residues within 4Å: Chain W: T.91, H.157 Ligand excluded by PLIP NI.48: 2 residues within 4Å: Chain X: T.91, H.157 Ligand excluded by PLIP

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
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

S
A

T
A

U
A

V
A

W
A

X
A

Ferritin

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