SMTL ID : 8j9m.1

Crystal Structure of Human H-Ferritin variant 123F assembling in solution3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.28, A:E.63, A:E.63, A:H.66 FE.2: 7 residues within 4Å: Chain A: H.174 Chain H: L.170, H.174 Chain P: H.174 Chain W: L.170, H.174 Ligands: FE.42 No protein-ligand interaction detected (PLIP) FE.3: 5 residues within 4Å: Chain A: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.108, H2O.1 FE.4: 5 residues within 4Å: Chain B: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.28, B:E.63, B:E.63, B:H.66 FE.5: 4 residues within 4Å: Chain B: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.6: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.28, C:E.63, C:E.63, C:H.66 FE.7: 4 residues within 4Å: Chain C: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.62, H2O.1 FE.8: 7 residues within 4Å: Chain C: H.174 Chain F: H.174 Chain I: H.174 Chain L: H.174 Ligands: FE.16, FE.24, FE.32 No protein-ligand interaction detected (PLIP) FE.9: 5 residues within 4Å: Chain D: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.28, D:E.63, D:E.63, D:H.66 FE.10: 7 residues within 4Å: Chain D: H.174 Chain K: L.170, H.174 Chain M: H.174 Chain T: L.170, H.174 Ligands: FE.34 No protein-ligand interaction detected (PLIP) FE.11: 5 residues within 4Å: Chain D: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.108, H2O.1 FE.12: 5 residues within 4Å: Chain E: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.28, E:E.63, E:E.63, E:H.66 FE.13: 4 residues within 4Å: Chain E: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.14: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.28, F:E.63, F:E.63, F:H.66 FE.15: 4 residues within 4Å: Chain F: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.62, H2O.2 FE.16: 7 residues within 4Å: Chain C: H.174 Chain F: H.174 Chain I: H.174 Chain L: H.174 Ligands: FE.8, FE.24, FE.32 No protein-ligand interaction detected (PLIP) FE.17: 5 residues within 4Å: Chain G: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.28, G:E.63, G:E.63, G:H.66 FE.18: 7 residues within 4Å: Chain E: L.170, H.174 Chain G: H.174 Chain Q: L.170, H.174 Chain S: H.174 Ligands: FE.50 No protein-ligand interaction detected (PLIP) FE.19: 5 residues within 4Å: Chain G: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.108, H2O.2 FE.20: 5 residues within 4Å: Chain H: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.28, H:E.63, H:E.63, H:H.66 FE.21: 4 residues within 4Å: Chain H: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.22: 4 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.28, I:E.63, I:E.63, I:H.66 FE.23: 4 residues within 4Å: Chain I: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.62, H2O.2 FE.24: 7 residues within 4Å: Chain C: H.174 Chain F: H.174 Chain I: H.174 Chain L: H.174 Ligands: FE.8, FE.16, FE.32 No protein-ligand interaction detected (PLIP) FE.25: 5 residues within 4Å: Chain J: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.28, J:E.63, J:E.63, J:H.66 FE.26: 7 residues within 4Å: Chain B: L.170, H.174 Chain J: H.174 Chain N: L.170, H.174 Chain V: H.174 Ligands: FE.58 No protein-ligand interaction detected (PLIP) FE.27: 5 residues within 4Å: Chain J: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.108, H2O.3 FE.28: 5 residues within 4Å: Chain K: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.28, K:E.63, K:E.63, K:H.66 FE.29: 4 residues within 4Å: Chain K: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.30: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.28, L:E.63, L:E.63, L:H.66 FE.31: 4 residues within 4Å: Chain L: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.62, H2O.3 FE.32: 7 residues within 4Å: Chain C: H.174 Chain F: H.174 Chain I: H.174 Chain L: H.174 Ligands: FE.8, FE.16, FE.24 No protein-ligand interaction detected (PLIP) FE.33: 5 residues within 4Å: Chain M: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:E.28, M:E.63, M:E.63, M:H.66 FE.34: 7 residues within 4Å: Chain D: H.174 Chain K: L.170, H.174 Chain M: H.174 Chain T: L.170, H.174 Ligands: FE.10 No protein-ligand interaction detected (PLIP) FE.35: 5 residues within 4Å: Chain M: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.108, H2O.3 FE.36: 5 residues within 4Å: Chain N: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.28, N:E.63, N:E.63, N:H.66 FE.37: 4 residues within 4Å: Chain N: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.38: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.28, O:E.63, O:E.63, O:H.66 FE.39: 4 residues within 4Å: Chain O: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.62, H2O.4 FE.40: 7 residues within 4Å: Chain O: H.174 Chain R: H.174 Chain U: H.174 Chain X: H.174 Ligands: FE.48, FE.56, FE.64 No protein-ligand interaction detected (PLIP) FE.41: 5 residues within 4Å: Chain P: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.28, P:E.63, P:E.63, P:H.66 FE.42: 7 residues within 4Å: Chain A: H.174 Chain H: L.170, H.174 Chain P: H.174 Chain W: L.170, H.174 Ligands: FE.2 No protein-ligand interaction detected (PLIP) FE.43: 5 residues within 4Å: Chain P: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.108, H2O.4 FE.44: 5 residues within 4Å: Chain Q: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.28, Q:E.63, Q:E.63, Q:H.66 FE.45: 4 residues within 4Å: Chain Q: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.46: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:E.28, R:E.63, R:E.63, R:H.66 FE.47: 4 residues within 4Å: Chain R: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.62, H2O.4 FE.48: 7 residues within 4Å: Chain O: H.174 Chain R: H.174 Chain U: H.174 Chain X: H.174 Ligands: FE.40, FE.56, FE.64 No protein-ligand interaction detected (PLIP) FE.49: 5 residues within 4Å: Chain S: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:E.28, S:E.63, S:E.63, S:H.66 FE.50: 7 residues within 4Å: Chain E: L.170, H.174 Chain G: H.174 Chain Q: L.170, H.174 Chain S: H.174 Ligands: FE.18 No protein-ligand interaction detected (PLIP) FE.51: 5 residues within 4Å: Chain S: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.108, H2O.4 FE.52: 5 residues within 4Å: Chain T: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.28, T:E.63, T:E.63, T:H.66 FE.53: 4 residues within 4Å: Chain T: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.54: 4 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.28, U:E.63, U:E.63, U:H.66 FE.55: 4 residues within 4Å: Chain U: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.62, H2O.5 FE.56: 7 residues within 4Å: Chain O: H.174 Chain R: H.174 Chain U: H.174 Chain X: H.174 Ligands: FE.40, FE.48, FE.64 No protein-ligand interaction detected (PLIP) FE.57: 5 residues within 4Å: Chain V: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:E.28, V:E.63, V:E.63, V:H.66 FE.58: 7 residues within 4Å: Chain B: L.170, H.174 Chain J: H.174 Chain N: L.170, H.174 Chain V: H.174 Ligands: FE.26 No protein-ligand interaction detected (PLIP) FE.59: 5 residues within 4Å: Chain V: Q.59, E.62, E.63, E.108, A.145 2 PLIP interactions: 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.108, H2O.5 FE.60: 5 residues within 4Å: Chain W: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.28, W:E.63, W:E.63, W:H.66 FE.61: 4 residues within 4Å: Chain W: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) FE.62: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:E.28, X:E.63, X:E.63, X:H.66 FE.63: 4 residues within 4Å: Chain X: Q.59, E.62, E.63, E.108 2 PLIP interactions: 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.62, H2O.6 FE.64: 7 residues within 4Å: Chain O: H.174 Chain R: H.174 Chain U: H.174 Chain X: H.174 Ligands: FE.40, FE.48, FE.56 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular pi-pi Interactions. Adv Sci (2023)

Release Date

2024-01-31

Peptides

Ferritin heavy chain: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

S
A

T
B

U
C

V
A

W
B

X
C

Ferritin heavy chain

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