SMTL ID : 5u1a.1 (1 other biounit)

Ferritin with Gc MtrE loop 1 inserted at His34

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-24-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.2: 6 residues within 4Å: Chain A: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.4: 5 residues within 4Å: Chain B: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.5: 6 residues within 4Å: Chain B: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain C: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.11: 4 residues within 4Å: Chain D: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.15: 6 residues within 4Å: Chain E: H.61, E.65, E.109, Q.142, E.145 Ligands: NA.17 Ligand excluded by PLIP NA.16: 6 residues within 4Å: Chain E: W.30, C.31, Y.32, T.33, S.47, Y.49 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain E: E.17, S.20, E.65, I.112 Ligands: NA.15 Ligand excluded by PLIP NA.20: 4 residues within 4Å: Chain F: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.21: 6 residues within 4Å: Chain F: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.22: 4 residues within 4Å: Chain F: T.86, S.87, I.88 Ligands: GOL.25 Ligand excluded by PLIP NA.23: 2 residues within 4Å: Chain F: E.78 Ligands: GOL.19 Ligand excluded by PLIP NA.28: 5 residues within 4Å: Chain G: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.29: 6 residues within 4Å: Chain G: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.31: 5 residues within 4Å: Chain H: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.32: 6 residues within 4Å: Chain H: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain I: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain J: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.42: 6 residues within 4Å: Chain K: H.61, E.65, E.109, Q.142, E.145 Ligands: NA.44 Ligand excluded by PLIP NA.43: 6 residues within 4Å: Chain K: W.30, C.31, Y.32, T.33, S.47, Y.49 Ligand excluded by PLIP NA.44: 5 residues within 4Å: Chain K: E.17, S.20, E.65, I.112 Ligands: NA.42 Ligand excluded by PLIP NA.47: 4 residues within 4Å: Chain L: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.48: 6 residues within 4Å: Chain L: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.49: 4 residues within 4Å: Chain L: T.86, S.87, I.88 Ligands: GOL.52 Ligand excluded by PLIP NA.50: 2 residues within 4Å: Chain L: E.78 Ligands: GOL.46 Ligand excluded by PLIP NA.55: 5 residues within 4Å: Chain M: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.56: 6 residues within 4Å: Chain M: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.58: 5 residues within 4Å: Chain N: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.59: 6 residues within 4Å: Chain N: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.61: 5 residues within 4Å: Chain O: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.65: 4 residues within 4Å: Chain P: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.69: 6 residues within 4Å: Chain Q: H.61, E.65, E.109, Q.142, E.145 Ligands: NA.71 Ligand excluded by PLIP NA.70: 6 residues within 4Å: Chain Q: W.30, C.31, Y.32, T.33, S.47, Y.49 Ligand excluded by PLIP NA.71: 5 residues within 4Å: Chain Q: E.17, S.20, E.65, I.112 Ligands: NA.69 Ligand excluded by PLIP NA.74: 4 residues within 4Å: Chain R: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.75: 6 residues within 4Å: Chain R: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.76: 4 residues within 4Å: Chain R: T.86, S.87, I.88 Ligands: GOL.79 Ligand excluded by PLIP NA.77: 2 residues within 4Å: Chain R: E.78 Ligands: GOL.73 Ligand excluded by PLIP NA.82: 5 residues within 4Å: Chain S: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.83: 6 residues within 4Å: Chain S: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.85: 5 residues within 4Å: Chain T: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.86: 6 residues within 4Å: Chain T: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.88: 5 residues within 4Å: Chain U: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.92: 4 residues within 4Å: Chain V: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.96: 6 residues within 4Å: Chain W: H.61, E.65, E.109, Q.142, E.145 Ligands: NA.98 Ligand excluded by PLIP NA.97: 6 residues within 4Å: Chain W: W.30, C.31, Y.32, T.33, S.47, Y.49 Ligand excluded by PLIP NA.98: 5 residues within 4Å: Chain W: E.17, S.20, E.65, I.112 Ligands: NA.96 Ligand excluded by PLIP NA.101: 4 residues within 4Å: Chain X: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.102: 6 residues within 4Å: Chain X: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.103: 4 residues within 4Å: Chain X: T.86, S.87, I.88 Ligands: GOL.106 Ligand excluded by PLIP NA.104: 2 residues within 4Å: Chain X: E.78 Ligands: GOL.100 Ligand excluded by PLIP

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

FE.3: 4 residues within 4Å: Chain A: H.164 Chain B: H.164 Chain D: H.164 Chain U: H.164 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain U, 1 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.164, U:H.164, A:H.164, D:H.164, H2O.16 FE.18: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.45, FE.72, FE.99 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.19, H2O.20, H2O.45, H2O.70, H2O.70, H2O.95 FE.24: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.51, FE.78, FE.105 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.25, H2O.25, H2O.50, H2O.75, H2O.76, H2O.101 FE.30: 4 residues within 4Å: Chain G: H.164 Chain H: H.164 Chain J: H.164 Chain O: H.164 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain O, 1 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: J:H.164, O:H.164, G:H.164, H:H.164, H2O.41 FE.45: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.18, FE.72, FE.99 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.19, H2O.45, H2O.45, H2O.70, H2O.95, H2O.96 FE.51: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.24, FE.78, FE.105 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.25, H2O.50, H2O.50, H2O.76, H2O.101, H2O.101 FE.57: 4 residues within 4Å: Chain C: H.164 Chain M: H.164 Chain N: H.164 Chain P: H.164 5 PLIP interactions: 1 interactions with chain N, 1 interactions with chain M, 1 interactions with chain C, 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: N:H.164, M:H.164, C:H.164, P:H.164, H2O.66 FE.72: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.18, FE.45, FE.99 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.19, H2O.45, H2O.45, H2O.70, H2O.70, H2O.95 FE.78: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.24, FE.51, FE.105 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.25, H2O.50, H2O.50, H2O.75, H2O.76, H2O.101 FE.84: 4 residues within 4Å: Chain I: H.164 Chain S: H.164 Chain T: H.164 Chain V: H.164 5 PLIP interactions: 1 interactions with chain T, 1 interactions with chain I, 1 interactions with chain S, 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: T:H.164, I:H.164, S:H.164, V:H.164, H2O.92 FE.99: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.18, FE.45, FE.72 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.19, H2O.20, H2O.45, H2O.70, H2O.95, H2O.96 FE.105: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.24, FE.51, FE.78 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.25, H2O.25, H2O.50, H2O.76, H2O.101, H2O.101

32 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain B: Y.32, T.56, F.59, D.60, K.181 Chain E: V.74, N.77 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain C: Y.32, T.56, F.59, K.181 Chain D: V.74, N.77 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain C: M.18, S.21, N.22, I.88 Chain D: M.18, Y.66, I.88 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain C: N.77 Chain D: Y.32, T.56, F.59 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain D: P.91, E.92, H.93 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain A: Y.32, T.56, F.59, D.60, K.181 Chain F: V.74, N.77 Ligands: NA.23 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain F: N.15, K.16, N.19, T.86 Ligands: NA.22, CL.27 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain A: V.74, N.77 Chain F: Y.32, T.56, F.59, K.181 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain H: Y.32, T.56, F.59, D.60, K.181 Chain K: V.74, N.77 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain I: Y.32, T.56, F.59, K.181 Chain J: V.74, N.77 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain I: M.18, S.21, N.22, I.88 Chain J: M.18, Y.66, I.88 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain I: N.77 Chain J: Y.32, T.56, F.59 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain J: P.91, E.92, H.93 Ligand excluded by PLIP GOL.46: 8 residues within 4Å: Chain G: Y.32, T.56, F.59, D.60, K.181 Chain L: V.74, N.77 Ligands: NA.50 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain L: N.15, K.16, N.19, T.86 Ligands: NA.49, CL.54 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain G: V.74, N.77 Chain L: Y.32, T.56, F.59, K.181 Ligand excluded by PLIP GOL.60: 7 residues within 4Å: Chain N: Y.32, T.56, F.59, D.60, K.181 Chain Q: V.74, N.77 Ligand excluded by PLIP GOL.62: 6 residues within 4Å: Chain O: Y.32, T.56, F.59, K.181 Chain P: V.74, N.77 Ligand excluded by PLIP GOL.63: 7 residues within 4Å: Chain O: M.18, S.21, N.22, I.88 Chain P: M.18, Y.66, I.88 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain O: N.77 Chain P: Y.32, T.56, F.59 Ligand excluded by PLIP GOL.67: 3 residues within 4Å: Chain P: P.91, E.92, H.93 Ligand excluded by PLIP GOL.73: 8 residues within 4Å: Chain M: Y.32, T.56, F.59, D.60, K.181 Chain R: V.74, N.77 Ligands: NA.77 Ligand excluded by PLIP GOL.79: 6 residues within 4Å: Chain R: N.15, K.16, N.19, T.86 Ligands: NA.76, CL.81 Ligand excluded by PLIP GOL.80: 6 residues within 4Å: Chain M: V.74, N.77 Chain R: Y.32, T.56, F.59, K.181 Ligand excluded by PLIP GOL.87: 7 residues within 4Å: Chain T: Y.32, T.56, F.59, D.60, K.181 Chain W: V.74, N.77 Ligand excluded by PLIP GOL.89: 6 residues within 4Å: Chain U: Y.32, T.56, F.59, K.181 Chain V: V.74, N.77 Ligand excluded by PLIP GOL.90: 7 residues within 4Å: Chain U: M.18, S.21, N.22, I.88 Chain V: M.18, Y.66, I.88 Ligand excluded by PLIP GOL.93: 4 residues within 4Å: Chain U: N.77 Chain V: Y.32, T.56, F.59 Ligand excluded by PLIP GOL.94: 3 residues within 4Å: Chain V: P.91, E.92, H.93 Ligand excluded by PLIP GOL.100: 8 residues within 4Å: Chain S: Y.32, T.56, F.59, D.60, K.181 Chain X: V.74, N.77 Ligands: NA.104 Ligand excluded by PLIP GOL.106: 6 residues within 4Å: Chain X: N.15, K.16, N.19, T.86 Ligands: NA.103, CL.108 Ligand excluded by PLIP GOL.107: 6 residues within 4Å: Chain S: V.74, N.77 Chain X: Y.32, T.56, F.59, K.181 Ligand excluded by PLIP

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

CL.10: 2 residues within 4Å: Chain C: T.86, S.87 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: S.87 Chain D: S.89, A.90 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain F: N.15, T.86 Ligands: GOL.25 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain I: T.86, S.87 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain I: S.87 Chain J: S.89, A.90 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain L: N.15, T.86 Ligands: GOL.52 Ligand excluded by PLIP CL.64: 2 residues within 4Å: Chain O: T.86, S.87 Ligand excluded by PLIP CL.68: 3 residues within 4Å: Chain O: S.87 Chain P: S.89, A.90 Ligand excluded by PLIP CL.81: 3 residues within 4Å: Chain R: N.15, T.86 Ligands: GOL.79 Ligand excluded by PLIP CL.91: 2 residues within 4Å: Chain U: T.86, S.87 Ligand excluded by PLIP CL.95: 3 residues within 4Å: Chain U: S.87 Chain V: S.89, A.90 Ligand excluded by PLIP CL.108: 3 residues within 4Å: Chain X: N.15, T.86 Ligands: GOL.106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structure-based design of ferritin nanoparticle immunogens displaying antigenic loops of Neisseria gonorrhoeae. FEBS Open Bio (2017)

Release Date

2017-10-11

Peptides

Ferritin,MtrE protein chimera: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Ferritin,MtrE protein chimera

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