SMTL ID : 9jiu.1

Ferritin mutant R63MeHis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-24-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: E.135 Chain H: E.135 Chain K: E.135 Ligand excluded by PLIP NA.2: 5 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 Ligands: NA.3 Ligand excluded by PLIP NA.3: 5 residues within 4Å: Chain A: E.63, H.66, E.108, Q.142 Ligands: NA.2 Ligand excluded by PLIP NA.5: 3 residues within 4Å: Chain B: E.135 Chain L: E.135 Chain S: E.135 Ligand excluded by PLIP NA.6: 3 residues within 4Å: Chain B: E.63, E.108, Q.142 Ligand excluded by PLIP NA.7: 3 residues within 4Å: Chain C: E.135 Chain I: E.135 Chain R: E.135 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain C: E.63, H.66, E.108, Q.142 Ligands: NA.9 Ligand excluded by PLIP NA.9: 5 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 Ligands: NA.8 Ligand excluded by PLIP NA.10: 3 residues within 4Å: Chain D: E.135 Chain E: E.135 Chain J: E.135 Ligand excluded by PLIP NA.11: 3 residues within 4Å: Chain D: E.63, E.108, Q.142 Ligand excluded by PLIP NA.13: 4 residues within 4Å: Chain E: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.14: 4 residues within 4Å: Chain F: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.16: 4 residues within 4Å: Chain G: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.17: 4 residues within 4Å: Chain H: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.19: 3 residues within 4Å: Chain I: E.63, E.108, Q.142 Ligand excluded by PLIP NA.21: 4 residues within 4Å: Chain J: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain K: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.25: 4 residues within 4Å: Chain L: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.26: 3 residues within 4Å: Chain M: E.135 Chain T: E.135 Chain W: E.135 Ligand excluded by PLIP NA.27: 5 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 Ligands: NA.28 Ligand excluded by PLIP NA.28: 5 residues within 4Å: Chain M: E.63, H.66, E.108, Q.142 Ligands: NA.27 Ligand excluded by PLIP NA.30: 3 residues within 4Å: Chain G: E.135 Chain N: E.135 Chain X: E.135 Ligand excluded by PLIP NA.31: 3 residues within 4Å: Chain N: E.63, E.108, Q.142 Ligand excluded by PLIP NA.32: 3 residues within 4Å: Chain F: E.135 Chain O: E.135 Chain U: E.135 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain O: E.63, H.66, E.108, Q.142 Ligands: NA.34 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 Ligands: NA.33 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain P: E.135 Chain Q: E.135 Chain V: E.135 Ligand excluded by PLIP NA.36: 3 residues within 4Å: Chain P: E.63, E.108, Q.142 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain Q: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain R: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain S: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain T: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.44: 3 residues within 4Å: Chain U: E.63, E.108, Q.142 Ligand excluded by PLIP NA.46: 4 residues within 4Å: Chain V: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.48: 4 residues within 4Å: Chain W: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP NA.50: 4 residues within 4Å: Chain X: E.63, H.66, E.108, Q.142 Ligand excluded by PLIP

14 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 12 residues within 4Å: Chain A: S.32, Y.33, S.60, H.64, I.86 Chain I: S.32, Y.33, L.36, S.60, H.64, I.86 Ligands: P6G.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:S.60 Hydrophobic interactions: I:L.36 P6G.12: 12 residues within 4Å: Chain D: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 Chain L: S.32, S.60, H.61, H.64, I.86 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain L Hydrogen bonds: D:S.60, L:S.60 P6G.15: 12 residues within 4Å: Chain E: S.32, Y.33, L.36, S.60, H.64, I.86 Chain G: S.32, Y.33, L.36, S.60, H.64, I.86 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:S.60, E:S.60 P6G.18: 12 residues within 4Å: Chain F: L.29, S.32, Y.33, L.36, S.60, H.64, I.86 Chain H: S.32, Y.33, S.60, H.64, I.86 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F Water bridges: H:H.61 Hydrogen bonds: F:S.60 P6G.20: 9 residues within 4Å: Chain A: S.32, S.60, H.61, H.64 Chain I: S.32, S.60, H.61, H.64 Ligands: P6G.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.32, A:S.60 P6G.22: 14 residues within 4Å: Chain C: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 Chain J: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain J Hydrogen bonds: C:S.60, J:S.60, J:S.60 P6G.24: 13 residues within 4Å: Chain B: S.32, Y.33, S.60, H.61, H.64, I.86 Chain K: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.60, B:H.61 P6G.29: 12 residues within 4Å: Chain M: S.32, Y.33, S.60, H.64, I.86 Chain U: S.32, Y.33, L.36, S.60, H.64, I.86 Ligands: P6G.45 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain M Hydrophobic interactions: U:L.36 Hydrogen bonds: M:S.60 P6G.37: 12 residues within 4Å: Chain P: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 Chain X: S.32, S.60, H.61, H.64, I.86 2 PLIP interactions: 1 interactions with chain X, 1 interactions with chain P Hydrogen bonds: X:S.60, P:S.60 P6G.40: 12 residues within 4Å: Chain Q: S.32, Y.33, L.36, S.60, H.64, I.86 Chain S: S.32, Y.33, L.36, S.60, H.64, I.86 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain S Hydrogen bonds: Q:S.60, S:S.60 P6G.43: 12 residues within 4Å: Chain R: L.29, S.32, Y.33, L.36, S.60, H.64, I.86 Chain T: S.32, Y.33, S.60, H.64, I.86 2 PLIP interactions: 1 interactions with chain T, 1 interactions with chain R Water bridges: T:H.61 Hydrogen bonds: R:S.60 P6G.45: 9 residues within 4Å: Chain M: S.32, S.60, H.61, H.64 Chain U: S.32, S.60, H.61, H.64 Ligands: P6G.29 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:S.32, M:S.60 P6G.47: 14 residues within 4Å: Chain O: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 Chain V: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 3 PLIP interactions: 1 interactions with chain O, 2 interactions with chain V Hydrogen bonds: O:S.60, V:S.60, V:S.60 P6G.49: 13 residues within 4Å: Chain N: S.32, Y.33, S.60, H.61, H.64, I.86 Chain W: S.32, Y.33, L.36, S.60, H.61, H.64, I.86 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:S.60, N:H.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsou, J.C. et al., Site-Specific Histidine Aza-Michael Addition in Proteins Enabled by a Ferritin-Based Metalloenzyme. J.Am.Chem.Soc. (2024)

Release Date

2024-12-04

Peptides

Ferritin heavy chain: 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 heavy chain