SMTL ID : 6h6u.1

Unitary crystal structure of the positively supercharged variant Ftn(pos) from human heavy chain ferritin (PEG 400 condition)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.28, A:E.63, H2O.1, H2O.1 FE.2: 5 residues within 4Å: Chain A: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.62, H2O.1 FE.3: 1 residues within 4Å: Chain A: E.62 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.62 FE.5: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.28, B:E.63, B:E.63, B:H.66 FE.6: 4 residues within 4Å: Chain B: Q.59, E.62, E.63, E.108 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.62 FE.7: 1 residues within 4Å: Chain B: E.62 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.62 FE.9: 5 residues within 4Å: Chain C: E.28, E.63, H.66, E.108, Q.142 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.28, C:E.63, C:E.63, C:H.66 FE.10: 4 residues within 4Å: Chain C: Q.59, E.62, E.63, E.141 No protein-ligand interaction detected (PLIP) FE.12: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.28, D:E.63, D:H.66 FE.13: 5 residues within 4Å: Chain D: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.62, D:E.63 FE.16: 5 residues within 4Å: Chain E: E.28, E.63, H.66, E.108, Q.142 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.28, E:E.63, E:E.63, E:H.66, H2O.3 FE.17: 5 residues within 4Å: Chain E: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.62 FE.18: 1 residues within 4Å: Chain E: E.62 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.62 FE.19: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.28, F:E.63, F:H.66, H2O.3, H2O.4 FE.20: 5 residues within 4Å: Chain F: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.62 FE.21: 4 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.28, G:E.63, H2O.4, H2O.4 FE.22: 5 residues within 4Å: Chain G: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.62, H2O.4 FE.23: 1 residues within 4Å: Chain G: E.62 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.62 FE.25: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.28, H:E.63, H:E.63, H:H.66 FE.26: 4 residues within 4Å: Chain H: Q.59, E.62, E.63, E.108 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.62 FE.27: 1 residues within 4Å: Chain H: E.62 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.62 FE.29: 5 residues within 4Å: Chain I: E.28, E.63, H.66, E.108, Q.142 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.28, I:E.63, I:E.63, I:H.66 FE.30: 4 residues within 4Å: Chain I: Q.59, E.62, E.63, E.141 No protein-ligand interaction detected (PLIP) FE.32: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.28, J:E.63, J:H.66 FE.33: 5 residues within 4Å: Chain J: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.62, J:E.63 FE.36: 5 residues within 4Å: Chain K: E.28, E.63, H.66, E.108, Q.142 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.28, K:E.63, K:E.63, K:H.66, H2O.7 FE.37: 5 residues within 4Å: Chain K: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.62 FE.38: 1 residues within 4Å: Chain K: E.62 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.62 FE.39: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.28, L:E.63, L:H.66, H2O.7, H2O.7 FE.40: 5 residues within 4Å: Chain L: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.62 FE.41: 4 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 4 PLIP interactions: 2 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, H2O.8, H2O.8 FE.42: 5 residues within 4Å: Chain M: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.62, H2O.8 FE.43: 1 residues within 4Å: Chain M: E.62 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.62 FE.45: 4 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.28, N:E.63, N:E.63, N:H.66 FE.46: 4 residues within 4Å: Chain N: Q.59, E.62, E.63, E.108 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.62 FE.47: 1 residues within 4Å: Chain N: E.62 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.62 FE.49: 5 residues within 4Å: Chain O: E.28, E.63, H.66, E.108, Q.142 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.28, O:E.63, O:E.63, O:H.66 FE.50: 4 residues within 4Å: Chain O: Q.59, E.62, E.63, E.141 No protein-ligand interaction detected (PLIP) FE.52: 4 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.28, P:E.63, P:H.66 FE.53: 5 residues within 4Å: Chain P: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:E.62, P:E.63 FE.56: 5 residues within 4Å: Chain Q: E.28, E.63, H.66, E.108, Q.142 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.28, Q:E.63, Q:E.63, Q:H.66, H2O.10 FE.57: 5 residues within 4Å: Chain Q: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.62 FE.58: 1 residues within 4Å: Chain Q: E.62 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.62 FE.59: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.28, R:E.63, R:H.66, H2O.10, H2O.10 FE.60: 5 residues within 4Å: Chain R: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.62 FE.61: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 4 PLIP interactions: 2 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, H2O.11, H2O.11 FE.62: 5 residues within 4Å: Chain S: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 1 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.62, H2O.11 FE.63: 1 residues within 4Å: Chain S: E.62 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:E.62 FE.65: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.28, T:E.63, T:E.63, T:H.66 FE.66: 4 residues within 4Å: Chain T: Q.59, E.62, E.63, E.108 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.62 FE.67: 1 residues within 4Å: Chain T: E.62 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.62 FE.69: 5 residues within 4Å: Chain U: E.28, E.63, H.66, E.108, Q.142 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.28, U:E.63, U:E.63, U:H.66 FE.70: 4 residues within 4Å: Chain U: Q.59, E.62, E.63, E.141 No protein-ligand interaction detected (PLIP) FE.72: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.28, V:E.63, V:H.66 FE.73: 5 residues within 4Å: Chain V: Q.59, E.62, E.63, E.108, E.141 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:E.62, V:E.63 FE.76: 5 residues within 4Å: Chain W: E.28, E.63, H.66, E.108, Q.142 5 PLIP interactions: 4 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:E.63, W:H.66, H2O.13 FE.77: 5 residues within 4Å: Chain W: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.62 FE.78: 1 residues within 4Å: Chain W: E.62 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.62 FE.79: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.28, X:E.63, X:H.66, H2O.14, H2O.14 FE.80: 5 residues within 4Å: Chain X: Q.59, E.62, E.63, E.108, E.141 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:E.62

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.61, R.64, E.65 Chain D: H.61, R.64 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.64, A:E.65, A:E.65, D:H.61, D:R.64 GOL.24: 5 residues within 4Å: Chain G: H.61, R.64, E.65 Chain J: H.61, R.64 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain G Hydrogen bonds: J:H.61, J:R.64, G:R.64, G:E.65, G:E.65 GOL.44: 5 residues within 4Å: Chain M: H.61, R.64, E.65 Chain P: H.61, R.64 5 PLIP interactions: 2 interactions with chain P, 3 interactions with chain M Hydrogen bonds: P:H.61, P:R.64, M:R.64, M:E.65, M:E.65 GOL.64: 5 residues within 4Å: Chain S: H.61, R.64, E.65 Chain V: H.61, R.64 5 PLIP interactions: 2 interactions with chain V, 3 interactions with chain S Hydrogen bonds: V:H.61, V:R.64, S:R.64, S:E.65, S:E.65

16 x CA: CALCIUM ION(Non-covalent)

CA.8: 7 residues within 4Å: Chain A: D.132, T.136 Chain B: D.132, T.136 Chain C: D.132, T.136 Ligands: CA.11 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:D.132, B:D.132, A:D.132 CA.11: 7 residues within 4Å: Chain A: D.132, E.135 Chain B: D.132, E.135 Chain C: D.132, E.135 Ligands: CA.8 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Metal complexes: C:D.132, C:E.135, A:E.135, B:D.132, B:E.135 CA.14: 7 residues within 4Å: Chain D: D.132, E.135 Chain E: D.132, E.135 Chain F: D.132, E.135 Ligands: CA.15 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 interactions with chain D Metal complexes: F:D.132, F:E.135, E:D.132, E:E.135, D:E.135 CA.15: 6 residues within 4Å: Chain D: D.132, T.136 Chain E: D.132, T.136 Chain F: D.132 Ligands: CA.14 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Metal complexes: F:D.132, D:D.132, E:D.132 CA.28: 7 residues within 4Å: Chain G: D.132, T.136 Chain H: D.132, T.136 Chain I: D.132, T.136 Ligands: CA.31 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I, 1 interactions with chain G Metal complexes: H:D.132, I:D.132, G:D.132 CA.31: 7 residues within 4Å: Chain G: D.132, E.135 Chain H: D.132, E.135 Chain I: D.132, E.135 Ligands: CA.28 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G, 2 interactions with chain H Metal complexes: I:D.132, I:E.135, G:E.135, H:D.132, H:E.135 CA.34: 7 residues within 4Å: Chain J: D.132, E.135 Chain K: D.132, E.135 Chain L: D.132, E.135 Ligands: CA.35 5 PLIP interactions: 1 interactions with chain J, 2 interactions with chain K, 2 interactions with chain L Metal complexes: J:E.135, K:D.132, K:E.135, L:D.132, L:E.135 CA.35: 6 residues within 4Å: Chain J: D.132, T.136 Chain K: D.132, T.136 Chain L: D.132 Ligands: CA.34 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 1 interactions with chain J Metal complexes: K:D.132, L:D.132, J:D.132 CA.48: 7 residues within 4Å: Chain M: D.132, T.136 Chain N: D.132, T.136 Chain O: D.132, T.136 Ligands: CA.51 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain M, 1 interactions with chain O Metal complexes: N:D.132, M:D.132, O:D.132 CA.51: 7 residues within 4Å: Chain M: D.132, E.135 Chain N: D.132, E.135 Chain O: D.132, E.135 Ligands: CA.48 5 PLIP interactions: 2 interactions with chain O, 2 interactions with chain N, 1 interactions with chain M Metal complexes: O:D.132, O:E.135, N:D.132, N:E.135, M:E.135 CA.54: 7 residues within 4Å: Chain P: D.132, E.135 Chain Q: D.132, E.135 Chain R: D.132, E.135 Ligands: CA.55 5 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain R, 1 interactions with chain P Metal complexes: Q:D.132, Q:E.135, R:D.132, R:E.135, P:E.135 CA.55: 6 residues within 4Å: Chain P: D.132, T.136 Chain Q: D.132, T.136 Chain R: D.132 Ligands: CA.54 3 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain P, 1 interactions with chain R Metal complexes: Q:D.132, P:D.132, R:D.132 CA.68: 7 residues within 4Å: Chain S: D.132, T.136 Chain T: D.132, T.136 Chain U: D.132, T.136 Ligands: CA.71 3 PLIP interactions: 1 interactions with chain T, 1 interactions with chain U, 1 interactions with chain S Metal complexes: T:D.132, U:D.132, S:D.132 CA.71: 7 residues within 4Å: Chain S: D.132, E.135 Chain T: D.132, E.135 Chain U: D.132, E.135 Ligands: CA.68 5 PLIP interactions: 2 interactions with chain T, 2 interactions with chain U, 1 interactions with chain S Metal complexes: T:D.132, T:E.135, U:D.132, U:E.135, S:E.135 CA.74: 7 residues within 4Å: Chain V: D.132, E.135 Chain W: D.132, E.135 Chain X: D.132, E.135 Ligands: CA.75 5 PLIP interactions: 2 interactions with chain W, 2 interactions with chain X, 1 interactions with chain V Metal complexes: W:D.132, W:E.135, X:D.132, X:E.135, V:E.135 CA.75: 6 residues within 4Å: Chain V: D.132, T.136 Chain W: D.132, T.136 Chain X: D.132 Ligands: CA.74 3 PLIP interactions: 1 interactions with chain W, 1 interactions with chain X, 1 interactions with chain V Metal complexes: W:D.132, X:D.132, V:D.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuenzle, M. et al., Self-assembly of protein crystals into different crystal structures using charged patches on oppositely charged ferritin protein containers. To Be Published

Release Date

2019-08-14

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
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 heavy chain

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