SMTL ID : 6j4j.1

soybean seed H-2 ferritin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-24-mer

Ligands

40 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.54, A:E.89, A:H.92, H2O.1, H2O.2 MG.2: 6 residues within 4Å: Chain A: D.162, E.165 Chain C: D.162, E.165 Chain T: D.162, E.165 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain T, 2 interactions with chain C Metal complexes: A:D.162, A:E.165, T:E.165, C:D.162, C:E.165 MG.3: 3 residues within 4Å: Chain B: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.54, B:E.89, B:H.92, H2O.4 MG.4: 3 residues within 4Å: Chain B: R.36, D.41, E.44 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.41, B:E.44 MG.5: 4 residues within 4Å: Chain C: E.54, E.89, H.92, T.141 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.54, C:E.89, C:H.92, H2O.7, H2O.7 MG.6: 6 residues within 4Å: Chain C: R.90, E.94 Chain D: H.62, S.86, E.87, R.90 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.94 MG.7: 6 residues within 4Å: Chain D: D.162, E.165 Chain E: D.162, E.165 Chain X: D.162, E.165 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain X, 1 interactions with chain D Metal complexes: E:D.162, E:E.165, X:D.162, X:E.165, D:E.165 MG.8: 3 residues within 4Å: Chain D: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.54, D:E.89, D:H.92, H2O.9, H2O.9 MG.9: 5 residues within 4Å: Chain E: E.54, E.89, H.92, T.141, Q.172 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.54, E:E.54, E:E.89, E:H.92 MG.10: 3 residues within 4Å: Chain F: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.54, F:E.89, F:H.92, H2O.14 MG.11: 3 residues within 4Å: Chain G: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.54, G:E.89, G:H.92, H2O.16, H2O.17 MG.12: 6 residues within 4Å: Chain G: D.162, E.165 Chain I: D.162, E.165 Chain N: D.162, E.165 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain N, 2 interactions with chain G Metal complexes: I:D.162, I:E.165, N:E.165, G:D.162, G:E.165 MG.13: 3 residues within 4Å: Chain H: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.54, H:E.89, H:H.92, H2O.19 MG.14: 3 residues within 4Å: Chain H: R.36, D.41, E.44 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.41, H:E.44 MG.15: 4 residues within 4Å: Chain I: E.54, E.89, H.92, T.141 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.54, I:E.89, I:H.92, H2O.22, H2O.23 MG.16: 6 residues within 4Å: Chain I: R.90, E.94 Chain J: H.62, S.86, E.87, R.90 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.94 MG.17: 6 residues within 4Å: Chain J: D.162, E.165 Chain K: D.162, E.165 Chain R: D.162, E.165 5 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J, 2 interactions with chain R Metal complexes: K:D.162, K:E.165, J:E.165, R:D.162, R:E.165 MG.18: 3 residues within 4Å: Chain J: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.54, J:E.89, J:H.92, H2O.25, H2O.25 MG.19: 5 residues within 4Å: Chain K: E.54, E.89, H.92, T.141, Q.172 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.54, K:E.54, K:E.89, K:H.92 MG.20: 3 residues within 4Å: Chain L: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.54, L:E.89, L:H.92, H2O.30 MG.21: 3 residues within 4Å: Chain M: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.54, M:E.89, M:H.92, H2O.32, H2O.33 MG.22: 6 residues within 4Å: Chain B: D.162, E.165 Chain M: D.162, E.165 Chain O: D.162, E.165 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain M, 2 interactions with chain O Metal complexes: B:E.165, M:D.162, M:E.165, O:D.162, O:E.165 MG.23: 3 residues within 4Å: Chain N: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.54, N:E.89, N:H.92, H2O.35 MG.24: 3 residues within 4Å: Chain N: R.36, D.41, E.44 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.41, N:E.44 MG.25: 4 residues within 4Å: Chain O: E.54, E.89, H.92, T.141 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.54, O:E.89, O:H.92, H2O.38, H2O.38 MG.26: 6 residues within 4Å: Chain O: R.90, E.94 Chain P: H.62, S.86, E.87, R.90 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:E.94 MG.27: 6 residues within 4Å: Chain F: D.162, E.165 Chain P: D.162, E.165 Chain Q: D.162, E.165 5 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain F, 1 interactions with chain P Metal complexes: Q:D.162, Q:E.165, F:D.162, F:E.165, P:E.165 MG.28: 3 residues within 4Å: Chain P: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.54, P:E.89, P:H.92, H2O.40, H2O.41 MG.29: 5 residues within 4Å: Chain Q: E.54, E.89, H.92, T.141, Q.172 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.54, Q:E.54, Q:E.89, Q:H.92 MG.30: 3 residues within 4Å: Chain R: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.54, R:E.89, R:H.92, H2O.45 MG.31: 3 residues within 4Å: Chain S: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.54, S:E.89, S:H.92, H2O.47, H2O.48 MG.32: 6 residues within 4Å: Chain H: D.162, E.165 Chain S: D.162, E.165 Chain U: D.162, E.165 5 PLIP interactions: 2 interactions with chain U, 2 interactions with chain S, 1 interactions with chain H Metal complexes: U:D.162, U:E.165, S:D.162, S:E.165, H:E.165 MG.33: 3 residues within 4Å: Chain T: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.54, T:E.89, T:H.92, H2O.50 MG.34: 3 residues within 4Å: Chain T: R.36, D.41, E.44 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:D.41, T:E.44 MG.35: 4 residues within 4Å: Chain U: E.54, E.89, H.92, T.141 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.54, U:E.89, U:H.92, H2O.54, H2O.54 MG.36: 6 residues within 4Å: Chain U: R.90, E.94 Chain V: H.62, S.86, E.87, R.90 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:E.94 MG.37: 6 residues within 4Å: Chain L: D.162, E.165 Chain V: D.162, E.165 Chain W: D.162, E.165 5 PLIP interactions: 2 interactions with chain L, 2 interactions with chain W, 1 interactions with chain V Metal complexes: L:D.162, L:E.165, W:D.162, W:E.165, V:E.165 MG.38: 3 residues within 4Å: Chain V: E.54, E.89, H.92 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.54, V:E.89, V:H.92, H2O.56, H2O.56 MG.39: 5 residues within 4Å: Chain W: E.54, E.89, H.92, T.141, Q.172 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.54, W:E.54, W:E.89, W:H.92 MG.40: 3 residues within 4Å: Chain X: E.54, E.89, H.92 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.54, X:E.89, X:H.92, H2O.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Thermostability of protein nanocages: the effect of natural extra peptide on the exterior surface. Rsc Adv (2019)

Release Date

2019-09-18

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
B

D
C

E
D

F
E

G
H

H
A

I
B

J
C

K
D

L
E

M
H

N
A

O
B

P
C

Q
D

R
E

S
H

T
A

U
B

V
C

W
D

X
E

Ferritin

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