SMTL ID : 4p18.1

Crystal Structure of frog M ferritin mutant D80K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-24-mer

Ligands

25 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: Y.35, E.50, K.53 Chain B: K.68 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain C: Y.35, E.50, K.53 Chain D: K.68 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain D: L.166, H.170 Chain F: L.166, H.170 Chain H: L.166, H.170 Chain L: L.166, H.170 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain D: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain F: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain E: K.68 Chain F: Y.35, H.46, E.50, K.53 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain G: Y.35, E.50, K.53 Chain H: K.68 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain G: K.68 Chain H: Y.35, H.46, E.50, K.53 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain J: R.40, E.89 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain J: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain L: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain M: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain N: Y.35, E.50, K.53 Chain P: K.68 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain N: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain K: K.68 Chain O: Y.35, E.50, K.53 Ligand excluded by PLIP SO4.71: 8 residues within 4Å: Chain I: L.166, H.170 Chain K: L.166, H.170 Chain M: L.166, H.170 Chain P: L.166, H.170 Ligand excluded by PLIP SO4.72: 3 residues within 4Å: Chain P: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.76: 8 residues within 4Å: Chain N: L.166, H.170 Chain Q: L.166, H.170 Chain S: L.166, H.170 Chain U: L.166, H.170 Ligand excluded by PLIP SO4.77: 5 residues within 4Å: Chain Q: Y.35, H.46, E.50, K.53 Chain R: K.68 Ligand excluded by PLIP SO4.80: 8 residues within 4Å: Chain G: L.166, H.170 Chain O: L.166, H.170 Chain R: L.166, H.170 Chain X: L.166, H.170 Ligand excluded by PLIP SO4.89: 8 residues within 4Å: Chain A: L.166, H.170 Chain C: L.166, H.170 Chain J: L.166, H.170 Chain T: L.166, H.170 Ligand excluded by PLIP SO4.90: 4 residues within 4Å: Chain S: K.68 Chain T: Y.35, E.50, K.53 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain U: R.6, Q.7, N.8 Ligand excluded by PLIP SO4.101: 8 residues within 4Å: Chain B: L.166, H.170 Chain E: L.166, H.170 Chain V: L.166, H.170 Chain W: L.166, H.170 Ligand excluded by PLIP SO4.102: 3 residues within 4Å: Chain W: R.6, Q.7, N.8 Ligand excluded by PLIP

51 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: F.38, D.39, A.44, L.45, H.46 Chain T: K.143, D.147 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain B: R.40, E.89 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain B: N.160, G.161, M.162 Chain E: R.154, L.155, G.156, N.160 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain B: N.47, K.169 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: P.158, E.159, G.161 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: R.154 Chain C: D.42, V.43, G.91, N.92, E.164 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain C: Y.69, K.72, H.125, D.128, F.129 Chain L: E.136 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain D: K.143, D.147 Chain F: D.39, A.44, H.46 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain E: P.158, E.159, G.161 Ligands: CL.103 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain F: K.72, H.125 Chain W: E.136, V.139, K.140 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain F: T.119, V.122, D.123, P.124, C.127 Chain W: H.115 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain F: V.2, S.3, R.6, G.74, R.76 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain G: P.158, E.159, G.161 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain H: K.65, K.68, Y.69, K.72, F.129 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain H: N.47, K.169 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain F: R.154 Chain H: V.43, L.45, G.91, N.92, E.164 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain I: V.2, S.3, R.6, G.74, R.76 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain I: E.136, V.139, K.140 Chain L: K.72, H.125 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain I: N.47, K.169, K.173 Chain P: H.170 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain J: V.2, S.3, R.6, E.14, G.74, G.75, R.76 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain K: K.65, K.68, Y.69, F.129 Ligand excluded by PLIP EDO.47: 2 residues within 4Å: Chain K: N.47, K.169 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain I: H.115 Chain L: T.119, V.122, D.123, P.124, C.127 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain L: S.3, G.74, R.76 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain M: P.158, E.159, G.161 Ligands: CL.34 Ligand excluded by PLIP EDO.58: 2 residues within 4Å: Chain M: N.47, K.169 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain M: E.86, R.87, W.90, A.99 Ligand excluded by PLIP EDO.60: 2 residues within 4Å: Chain M: H.10, S.11 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain M: R.87, D.88, E.89 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain M: G.156, E.159, N.160 Ligands: CL.44 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain M: V.2, S.3, R.6, G.74, R.76 Ligand excluded by PLIP EDO.69: 5 residues within 4Å: Chain O: V.2, S.3, R.6, G.74, R.76 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain M: H.115, T.119 Chain O: V.122, P.124, C.127 Ligand excluded by PLIP EDO.74: 4 residues within 4Å: Chain P: D.128 Chain S: E.131, S.132, E.136 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain I: D.39 Chain J: K.68, K.72 Chain P: K.143, D.147 Ligand excluded by PLIP EDO.78: 5 residues within 4Å: Chain Q: K.65, K.68, Y.69, K.72, F.129 Ligand excluded by PLIP EDO.79: 6 residues within 4Å: Chain N: R.154 Chain Q: D.42, V.43, G.91, N.92, E.164 Ligand excluded by PLIP EDO.83: 6 residues within 4Å: Chain R: D.42, V.43, G.91, N.92, E.164 Chain X: R.154 Ligand excluded by PLIP EDO.84: 7 residues within 4Å: Chain Q: R.76, V.77, V.78 Chain R: F.37, R.40, D.88, E.89 Ligand excluded by PLIP EDO.86: 3 residues within 4Å: Chain S: A.44, H.46 Chain U: D.147 Ligand excluded by PLIP EDO.87: 3 residues within 4Å: Chain S: D.42 Chain T: Q.4 Chain U: T.150 Ligand excluded by PLIP EDO.91: 6 residues within 4Å: Chain J: R.154 Chain T: D.42, V.43, G.91, N.92, E.164 Ligand excluded by PLIP EDO.92: 1 residues within 4Å: Chain T: N.8 Ligand excluded by PLIP EDO.93: 5 residues within 4Å: Chain B: V.122, P.124, C.127 Chain T: H.115, T.119 Ligand excluded by PLIP EDO.94: 5 residues within 4Å: Chain T: V.2, S.3, R.6, G.74, R.76 Ligand excluded by PLIP EDO.98: 1 residues within 4Å: Chain U: K.84 Ligand excluded by PLIP EDO.99: 4 residues within 4Å: Chain V: K.143, D.147 Chain W: A.44, H.46 Ligand excluded by PLIP EDO.100: 3 residues within 4Å: Chain V: R.6, Q.7, N.8 Ligand excluded by PLIP EDO.104: 5 residues within 4Å: Chain W: V.2, S.3, R.6, G.74, R.76 Ligand excluded by PLIP EDO.108: 6 residues within 4Å: Chain G: R.154 Chain X: D.42, V.43, G.91, N.92, E.164 Ligand excluded by PLIP EDO.109: 3 residues within 4Å: Chain X: R.87, D.88, E.89 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: K.72, H.125 Chain E: E.136, V.139, K.140 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Water bridges: A:K.72, A:K.72 Salt bridges: A:K.72, A:H.125, E:K.140 Hydrophobic interactions: E:E.136 ACT.88: 5 residues within 4Å: Chain S: Y.35, H.46, E.50, K.53 Chain T: K.68 3 PLIP interactions: 2 interactions with chain S, 1 interactions with chain T Hydrophobic interactions: S:Y.35 Salt bridges: S:K.53, T:K.68

31 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain B: N.8 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: N.22, Y.26, K.81, I.82, K.83 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain C: N.8 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: G.91, N.92, E.164 Chain L: R.154 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain D: Y.35, E.50 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain E: N.8 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain G: E.136, V.139 Chain W: H.125 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain G: N.8 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain I: R.154 Chain M: G.161, E.164 Ligands: EDO.57 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain J: G.156, L.157, P.158, E.159 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain I: K.68 Chain J: Y.35, E.50, K.53 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain K: G.156, L.157, P.158, E.159 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain K: M.162 Chain M: R.154, L.155, G.156 Ligands: EDO.62 Ligand excluded by PLIP CL.45: 1 residues within 4Å: Chain K: N.8 Ligand excluded by PLIP CL.49: 1 residues within 4Å: Chain M: K.84 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain L: Y.35, E.50 Chain M: K.68 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain I: D.147 Chain M: A.44, H.46 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain L: Y.29 Chain M: L.21, N.22, L.79, Q.80 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain M: L.25, S.28, Y.29 Ligand excluded by PLIP CL.66: 3 residues within 4Å: Chain N: A.44 Chain S: K.143, D.147 Ligand excluded by PLIP CL.68: 1 residues within 4Å: Chain O: N.8 Ligand excluded by PLIP CL.73: 5 residues within 4Å: Chain J: K.72, H.125 Chain P: E.136, V.139, K.140 Ligand excluded by PLIP CL.81: 2 residues within 4Å: Chain R: L.94, Q.98 Ligand excluded by PLIP CL.82: 3 residues within 4Å: Chain R: Y.35, E.50, K.53 Ligand excluded by PLIP CL.85: 2 residues within 4Å: Chain S: Q.7, N.8 Ligand excluded by PLIP CL.96: 3 residues within 4Å: Chain U: A.99, Q.102, L.103 Ligand excluded by PLIP CL.97: 1 residues within 4Å: Chain U: E.50 Ligand excluded by PLIP CL.103: 4 residues within 4Å: Chain E: G.161, E.164 Chain W: R.154 Ligands: EDO.20 Ligand excluded by PLIP CL.105: 1 residues within 4Å: Chain X: R.40 Ligand excluded by PLIP CL.106: 1 residues within 4Å: Chain X: N.8 Ligand excluded by PLIP CL.107: 4 residues within 4Å: Chain W: K.68 Chain X: Y.35, E.50, K.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernacchioni, C. et al., Loop electrostatics modulates the intersubunit interactions in ferritin. Acs Chem.Biol. (2014)

Release Date

2014-10-01

Peptides

Ferritin, middle subunit: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
M

F
N

G
O

H
P

I
S

J
T

K
E

L
F

M
G

N
H

O
I

P
J

Q
K

R
L

S
Q

T
R

U
U

V
V

W
W

X
X

Ferritin, middle subunit