SMTL ID : 5u1a.2 (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

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

NA.1: 4 residues within 4Å: Chain A: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.2: 7 residues within 4Å: Chain A: W.30, C.31, Y.32, T.33, G.34, S.47, Y.49 Ligand excluded by PLIP NA.5: 5 residues within 4Å: Chain A: N.80 Chain F: Y.32, T.33, Y.49, S.50 Ligand excluded by PLIP NA.6: 5 residues within 4Å: Chain B: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.7: 6 residues within 4Å: Chain B: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain B: Y.32, T.33, Y.49, S.50 Chain E: N.80 Ligand excluded by PLIP NA.10: 3 residues within 4Å: Chain B: S.50 Chain D: D.151, D.154 Ligand excluded by PLIP NA.11: 5 residues within 4Å: Chain C: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.12: 4 residues within 4Å: Chain C: D.151, D.154 Chain M: S.50 Chain R: N.80 Ligand excluded by PLIP NA.15: 5 residues within 4Å: Chain D: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.16: 5 residues within 4Å: Chain E: E.65, E.109, Q.142, E.145 Ligands: NA.17 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain E: E.17, S.20, E.65, I.112 Ligands: NA.16 Ligand excluded by PLIP NA.20: 3 residues within 4Å: Chain F: T.86, S.87, I.88 Ligand excluded by PLIP NA.21: 4 residues within 4Å: Chain F: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.22: 2 residues within 4Å: Chain F: N.19, S.89 Ligand excluded by PLIP NA.23: 1 residues within 4Å: Chain F: E.78 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain F: L.2, S.3, D.128 Ligands: CL.29 Ligand excluded by PLIP NA.30: 4 residues within 4Å: Chain G: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.31: 7 residues within 4Å: Chain G: W.30, C.31, Y.32, T.33, G.34, S.47, Y.49 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain G: N.80 Chain L: Y.32, T.33, Y.49, S.50 Ligand excluded by PLIP NA.35: 5 residues within 4Å: Chain H: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.36: 6 residues within 4Å: Chain H: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.37: 5 residues within 4Å: Chain H: Y.32, T.33, Y.49, S.50 Chain K: N.80 Ligand excluded by PLIP NA.39: 3 residues within 4Å: Chain H: S.50 Chain J: D.151, D.154 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain I: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain I: D.151, D.154 Chain S: S.50 Chain X: N.80 Ligand excluded by PLIP NA.44: 5 residues within 4Å: Chain J: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.45: 5 residues within 4Å: Chain K: E.65, E.109, Q.142, E.145 Ligands: NA.46 Ligand excluded by PLIP NA.46: 5 residues within 4Å: Chain K: E.17, S.20, E.65, I.112 Ligands: NA.45 Ligand excluded by PLIP NA.49: 3 residues within 4Å: Chain L: T.86, S.87, I.88 Ligand excluded by PLIP NA.50: 4 residues within 4Å: Chain L: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.51: 2 residues within 4Å: Chain L: N.19, S.89 Ligand excluded by PLIP NA.52: 1 residues within 4Å: Chain L: E.78 Ligand excluded by PLIP NA.53: 4 residues within 4Å: Chain L: L.2, S.3, D.128 Ligands: CL.58 Ligand excluded by PLIP NA.59: 4 residues within 4Å: Chain M: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.60: 7 residues within 4Å: Chain M: W.30, C.31, Y.32, T.33, G.34, S.47, Y.49 Ligand excluded by PLIP NA.63: 5 residues within 4Å: Chain M: N.80 Chain R: Y.32, T.33, Y.49, S.50 Ligand excluded by PLIP NA.64: 5 residues within 4Å: Chain N: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.65: 6 residues within 4Å: Chain N: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.66: 5 residues within 4Å: Chain N: Y.32, T.33, Y.49, S.50 Chain Q: N.80 Ligand excluded by PLIP NA.68: 3 residues within 4Å: Chain N: S.50 Chain P: D.151, D.154 Ligand excluded by PLIP NA.69: 5 residues within 4Å: Chain O: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.70: 4 residues within 4Å: Chain G: S.50 Chain L: N.80 Chain O: D.151, D.154 Ligand excluded by PLIP NA.73: 5 residues within 4Å: Chain P: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.74: 5 residues within 4Å: Chain Q: E.65, E.109, Q.142, E.145 Ligands: NA.75 Ligand excluded by PLIP NA.75: 5 residues within 4Å: Chain Q: E.17, S.20, E.65, I.112 Ligands: NA.74 Ligand excluded by PLIP NA.78: 3 residues within 4Å: Chain R: T.86, S.87, I.88 Ligand excluded by PLIP NA.79: 4 residues within 4Å: Chain R: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.80: 2 residues within 4Å: Chain R: N.19, S.89 Ligand excluded by PLIP NA.81: 1 residues within 4Å: Chain R: E.78 Ligand excluded by PLIP NA.82: 4 residues within 4Å: Chain R: L.2, S.3, D.128 Ligands: CL.87 Ligand excluded by PLIP NA.88: 4 residues within 4Å: Chain S: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.89: 7 residues within 4Å: Chain S: W.30, C.31, Y.32, T.33, G.34, S.47, Y.49 Ligand excluded by PLIP NA.92: 5 residues within 4Å: Chain S: N.80 Chain X: Y.32, T.33, Y.49, S.50 Ligand excluded by PLIP NA.93: 5 residues within 4Å: Chain T: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.94: 6 residues within 4Å: Chain T: W.30, C.31, Y.32, T.33, G.34, Y.49 Ligand excluded by PLIP NA.95: 5 residues within 4Å: Chain T: Y.32, T.33, Y.49, S.50 Chain W: N.80 Ligand excluded by PLIP NA.97: 3 residues within 4Å: Chain T: S.50 Chain V: D.151, D.154 Ligand excluded by PLIP NA.98: 5 residues within 4Å: Chain U: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.99: 4 residues within 4Å: Chain A: S.50 Chain F: N.80 Chain U: D.151, D.154 Ligand excluded by PLIP NA.102: 5 residues within 4Å: Chain V: H.61, E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.103: 5 residues within 4Å: Chain W: E.65, E.109, Q.142, E.145 Ligands: NA.104 Ligand excluded by PLIP NA.104: 5 residues within 4Å: Chain W: E.17, S.20, E.65, I.112 Ligands: NA.103 Ligand excluded by PLIP NA.107: 3 residues within 4Å: Chain X: T.86, S.87, I.88 Ligand excluded by PLIP NA.108: 4 residues within 4Å: Chain X: E.65, E.109, Q.142, E.145 Ligand excluded by PLIP NA.109: 2 residues within 4Å: Chain X: N.19, S.89 Ligand excluded by PLIP NA.110: 1 residues within 4Å: Chain X: E.78 Ligand excluded by PLIP NA.111: 4 residues within 4Å: Chain X: L.2, S.3, D.128 Ligands: CL.116 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 U, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: U:H.164, A:H.164, D:H.164, B:H.164, H2O.5 FE.18: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.47, FE.76, FE.105 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain W Metal complexes: K:H.164, Q:H.164, E:H.164, W:H.164 FE.25: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.54, FE.83, FE.112 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.28, H2O.28, H2O.56, H2O.56, H2O.84, H2O.85 FE.32: 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 G, 1 interactions with chain H, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: J:H.164, G:H.164, H:H.164, O:H.164, H2O.33 FE.47: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.18, FE.76, FE.105 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain W Metal complexes: K:H.164, Q:H.164, E:H.164, W:H.164 FE.54: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.25, FE.83, FE.112 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.28, H2O.28, H2O.56, H2O.56, H2O.113, H2O.113 FE.61: 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 P, 1 interactions with chain M, 1 interactions with chain C, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: P:H.164, M:H.164, C:H.164, N:H.164, H2O.62 FE.76: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.18, FE.47, FE.105 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain W Metal complexes: K:H.164, Q:H.164, E:H.164, W:H.164 FE.83: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.25, FE.54, FE.112 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.56, H2O.56, H2O.84, H2O.85, H2O.113, H2O.113 FE.90: 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 V, 1 interactions with chain S, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: T:H.164, V:H.164, S:H.164, I:H.164, H2O.90 FE.105: 7 residues within 4Å: Chain E: H.164 Chain K: H.164 Chain Q: H.164 Chain W: H.164 Ligands: FE.18, FE.47, FE.76 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain W Metal complexes: K:H.164, Q:H.164, E:H.164, W:H.164 FE.112: 7 residues within 4Å: Chain F: H.164 Chain L: H.164 Chain R: H.164 Chain X: H.164 Ligands: FE.25, FE.54, FE.83 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.28, H2O.28, H2O.84, H2O.85, H2O.113, H2O.113

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

CL.4: 4 residues within 4Å: Chain A: W.30, G.34, K.94, F.95 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain E: E.12, T.86 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain F: N.15, T.86 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain F: F.95, E.96, Q.100, K.104 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain F: L.2, D.128, A.130, T.131 Ligands: NA.24 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain G: W.30, G.34, K.94, F.95 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain K: E.12, T.86 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain L: N.15, T.86 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain L: F.95, E.96, Q.100, K.104 Ligand excluded by PLIP CL.58: 5 residues within 4Å: Chain L: L.2, D.128, A.130, T.131 Ligands: NA.53 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain M: W.30, G.34, K.94, F.95 Ligand excluded by PLIP CL.77: 2 residues within 4Å: Chain Q: E.12, T.86 Ligand excluded by PLIP CL.85: 2 residues within 4Å: Chain R: N.15, T.86 Ligand excluded by PLIP CL.86: 4 residues within 4Å: Chain R: F.95, E.96, Q.100, K.104 Ligand excluded by PLIP CL.87: 5 residues within 4Å: Chain R: L.2, D.128, A.130, T.131 Ligands: NA.82 Ligand excluded by PLIP CL.91: 4 residues within 4Å: Chain S: W.30, G.34, K.94, F.95 Ligand excluded by PLIP CL.106: 2 residues within 4Å: Chain W: E.12, T.86 Ligand excluded by PLIP CL.114: 2 residues within 4Å: Chain X: N.15, T.86 Ligand excluded by PLIP CL.115: 4 residues within 4Å: Chain X: F.95, E.96, Q.100, K.104 Ligand excluded by PLIP CL.116: 5 residues within 4Å: Chain X: L.2, D.128, A.130, T.131 Ligands: NA.111 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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.13: 8 residues within 4Å: Chain C: M.18, S.21, N.22, Y.66 Chain D: M.18, S.21, N.22, Y.66 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain C: Y.32, T.56, F.59, K.181 Chain D: N.77 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain A: V.74, N.77 Chain F: Y.32, T.56, F.59, D.60, K.181 Ligand excluded by PLIP GOL.38: 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.42: 8 residues within 4Å: Chain I: M.18, S.21, N.22, Y.66 Chain J: M.18, S.21, N.22, Y.66 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain I: Y.32, T.56, F.59, K.181 Chain J: N.77 Ligand excluded by PLIP GOL.55: 7 residues within 4Å: Chain G: V.74, N.77 Chain L: Y.32, T.56, F.59, D.60, K.181 Ligand excluded by PLIP GOL.67: 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.71: 8 residues within 4Å: Chain O: M.18, S.21, N.22, Y.66 Chain P: M.18, S.21, N.22, Y.66 Ligand excluded by PLIP GOL.72: 5 residues within 4Å: Chain O: Y.32, T.56, F.59, K.181 Chain P: N.77 Ligand excluded by PLIP GOL.84: 7 residues within 4Å: Chain M: V.74, N.77 Chain R: Y.32, T.56, F.59, D.60, K.181 Ligand excluded by PLIP GOL.96: 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.100: 8 residues within 4Å: Chain U: M.18, S.21, N.22, Y.66 Chain V: M.18, S.21, N.22, Y.66 Ligand excluded by PLIP GOL.101: 5 residues within 4Å: Chain U: Y.32, T.56, F.59, K.181 Chain V: N.77 Ligand excluded by PLIP GOL.113: 7 residues within 4Å: Chain S: V.74, N.77 Chain X: Y.32, T.56, F.59, D.60, K.181 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
G

B
H

C
I

D
J

E
K

F
L

G
G

H
H

I
I

J
J

K
K

L
L

M
G

N
H

O
I

P
J

Q
K

R
L

S
G

T
H

U
I

V
J

W
K

X
L

Ferritin,MtrE protein chimera

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