SMTL ID : 4nwp.1

Computationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21, Crystallized in Space Group R32

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-12-12-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.134 Chain P: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: S.25 Chain Q: T.131, R.134 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: W.86, K.89, L.90, R.93 Ligand excluded by PLIP SO4.4: 11 residues within 4Å: Chain A: E.29, R.124, K.128 Chain I: E.29, R.124, K.128 Chain Q: E.29, R.124, K.128 Ligands: SO4.33, SO4.62 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain A: Y.47 Chain I: Y.47, L.110 Chain Q: Y.47, L.110 Ligands: SO4.34, SO4.63 Ligand excluded by PLIP SO4.6: 9 residues within 4Å: Chain B: E.29, R.124, K.128 Chain C: E.29, R.124, K.128 Chain D: E.29, R.124, K.128 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: T.131, R.134 Chain C: S.25 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain B: H.46, K.53 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain C: W.86, L.90, R.93 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain C: T.131, R.134 Chain D: S.25 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain C: H.46, K.53 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: S.25 Chain D: T.131, R.134 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain D: H.46, K.53 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: Y.47 Chain C: Y.47, L.110 Chain D: Y.47 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: R.134 Chain E: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain E: L.69, R.72, R.111 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain E: R.107 Chain M: R.107 Chain U: R.107 Ligands: SO4.46, SO4.75 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain E: P.2, H.3, D.39, K.41, Y.114 Chain M: Q.101, S.103 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain F: R.107 Chain G: R.107 Chain P: R.107 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain F: L.69, R.72, R.111 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain F: D.73, I.74, R.77 Chain J: R.134 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain F: P.2, H.3, D.39, K.41, L.69, Y.114 Chain G: S.103 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: R.134 Chain G: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.24: 9 residues within 4Å: Chain G: P.2, H.3, D.39, K.41, M.109, Y.114, K.116 Chain P: S.103 Ligands: SO4.25 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain G: Q.34, L.69, R.72, R.111 Ligands: SO4.24 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain H: R.51 Chain W: G.19 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain H: Q.34, F.35, L.69, R.72, R.111 Ligands: SO4.28 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain H: P.2, H.3, D.39, K.41, Y.114, K.116 Ligands: SO4.27 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain I: R.134 Chain X: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain A: T.131, R.134 Chain I: S.25 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain I: W.86, K.89, L.90, R.93 Ligand excluded by PLIP SO4.33: 11 residues within 4Å: Chain A: E.29, R.124, K.128 Chain I: E.29, R.124, K.128 Chain Q: E.29, R.124, K.128 Ligands: SO4.4, SO4.62 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain A: Y.47, L.110 Chain I: Y.47 Chain Q: Y.47, L.110 Ligands: SO4.5, SO4.63 Ligand excluded by PLIP SO4.35: 9 residues within 4Å: Chain J: E.29, R.124, K.128 Chain K: E.29, R.124, K.128 Chain L: E.29, R.124, K.128 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain J: T.131, R.134 Chain K: S.25 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain J: H.46, K.53 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain K: W.86, L.90, R.93 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain K: T.131, R.134 Chain L: S.25 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain K: H.46, K.53 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain J: S.25 Chain L: T.131, R.134 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain L: H.46, K.53 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain J: Y.47 Chain K: Y.47, L.110 Chain L: Y.47 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain K: R.134 Chain M: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain M: L.69, R.72, R.111 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain E: R.107 Chain M: R.107 Chain U: R.107 Ligands: SO4.17, SO4.75 Ligand excluded by PLIP SO4.47: 7 residues within 4Å: Chain M: P.2, H.3, D.39, K.41, Y.114 Chain U: Q.101, S.103 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain N: R.107 Chain O: R.107 Chain X: R.107 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain N: L.69, R.72, R.111 Ligand excluded by PLIP SO4.50: 4 residues within 4Å: Chain N: D.73, I.74, R.77 Chain R: R.134 Ligand excluded by PLIP SO4.51: 7 residues within 4Å: Chain N: P.2, H.3, D.39, K.41, L.69, Y.114 Chain O: S.103 Ligand excluded by PLIP SO4.52: 5 residues within 4Å: Chain L: R.134 Chain O: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.53: 9 residues within 4Å: Chain O: P.2, H.3, D.39, K.41, M.109, Y.114, K.116 Chain X: S.103 Ligands: SO4.54 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain O: Q.34, L.69, R.72, R.111 Ligands: SO4.53 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain G: G.19 Chain P: R.51 Ligand excluded by PLIP SO4.56: 6 residues within 4Å: Chain P: Q.34, F.35, L.69, R.72, R.111 Ligands: SO4.57 Ligand excluded by PLIP SO4.57: 7 residues within 4Å: Chain P: P.2, H.3, D.39, K.41, Y.114, K.116 Ligands: SO4.56 Ligand excluded by PLIP SO4.59: 5 residues within 4Å: Chain H: R.72, D.73, I.74, R.77 Chain Q: R.134 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain I: T.131, R.134 Chain Q: S.25 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain Q: W.86, K.89, L.90, R.93 Ligand excluded by PLIP SO4.62: 11 residues within 4Å: Chain A: E.29, R.124, K.128 Chain I: E.29, R.124, K.128 Chain Q: E.29, R.124, K.128 Ligands: SO4.4, SO4.33 Ligand excluded by PLIP SO4.63: 7 residues within 4Å: Chain A: Y.47, L.110 Chain I: Y.47, L.110 Chain Q: Y.47 Ligands: SO4.5, SO4.34 Ligand excluded by PLIP SO4.64: 9 residues within 4Å: Chain R: E.29, R.124, K.128 Chain S: E.29, R.124, K.128 Chain T: E.29, R.124, K.128 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain R: T.131, R.134 Chain S: S.25 Ligand excluded by PLIP SO4.66: 2 residues within 4Å: Chain R: H.46, K.53 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain S: W.86, L.90, R.93 Ligand excluded by PLIP SO4.68: 3 residues within 4Å: Chain S: T.131, R.134 Chain T: S.25 Ligand excluded by PLIP SO4.69: 2 residues within 4Å: Chain S: H.46, K.53 Ligand excluded by PLIP SO4.70: 3 residues within 4Å: Chain R: S.25 Chain T: T.131, R.134 Ligand excluded by PLIP SO4.71: 2 residues within 4Å: Chain T: H.46, K.53 Ligand excluded by PLIP SO4.72: 4 residues within 4Å: Chain R: Y.47 Chain S: Y.47, L.110 Chain T: Y.47 Ligand excluded by PLIP SO4.73: 5 residues within 4Å: Chain S: R.134 Chain U: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.74: 3 residues within 4Å: Chain U: L.69, R.72, R.111 Ligand excluded by PLIP SO4.75: 5 residues within 4Å: Chain E: R.107 Chain M: R.107 Chain U: R.107 Ligands: SO4.17, SO4.46 Ligand excluded by PLIP SO4.76: 7 residues within 4Å: Chain E: Q.101, S.103 Chain U: P.2, H.3, D.39, K.41, Y.114 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain H: R.107 Chain V: R.107 Chain W: R.107 Ligand excluded by PLIP SO4.78: 3 residues within 4Å: Chain V: L.69, R.72, R.111 Ligand excluded by PLIP SO4.79: 4 residues within 4Å: Chain B: R.134 Chain V: D.73, I.74, R.77 Ligand excluded by PLIP SO4.80: 7 residues within 4Å: Chain V: P.2, H.3, D.39, K.41, L.69, Y.114 Chain W: S.103 Ligand excluded by PLIP SO4.81: 5 residues within 4Å: Chain T: R.134 Chain W: R.72, D.73, I.74, R.77 Ligand excluded by PLIP SO4.82: 9 residues within 4Å: Chain H: S.103 Chain W: P.2, H.3, D.39, K.41, M.109, Y.114, K.116 Ligands: SO4.83 Ligand excluded by PLIP SO4.83: 5 residues within 4Å: Chain W: Q.34, L.69, R.72, R.111 Ligands: SO4.82 Ligand excluded by PLIP SO4.84: 2 residues within 4Å: Chain O: G.19 Chain X: R.51 Ligand excluded by PLIP SO4.85: 6 residues within 4Å: Chain X: Q.34, F.35, L.69, R.72, R.111 Ligands: SO4.86 Ligand excluded by PLIP SO4.86: 7 residues within 4Å: Chain X: P.2, H.3, D.39, K.41, Y.114, K.116 Ligands: SO4.85 Ligand excluded by PLIP

3 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.29: 5 residues within 4Å: Chain H: E.105, V.106, R.107 Chain W: M.109, E.110 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain W Hydrogen bonds: H:E.105, H:E.105, W:E.110 Water bridges: H:V.106, H:E.108, W:R.107 NH4.58: 5 residues within 4Å: Chain G: M.109, E.110 Chain P: E.105, V.106, R.107 6 PLIP interactions: 4 interactions with chain P, 2 interactions with chain G Hydrogen bonds: P:E.105, P:E.105, G:E.110 Water bridges: P:V.106, P:E.108, G:R.107 NH4.87: 5 residues within 4Å: Chain O: M.109, E.110 Chain X: E.105, V.106, R.107 6 PLIP interactions: 4 interactions with chain X, 2 interactions with chain O Hydrogen bonds: X:E.105, X:E.105, O:E.110 Water bridges: X:V.106, X:E.108, O:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

King, N.P. et al., Accurate design of co-assembling multi-component protein nanomaterials. Nature (2014)

Release Date

2014-05-28

Peptides

Putative uncharacterized protein: ABCDIJKLQRST
Uncharacterized protein: EFGHMNOPUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

I
A

J
B

K
C

L
D

Q
A

R
B

S
C

T
D

E
E

F
F

G
G

H
H

M
E

N
F

O
G

P
H

U
E

V
F

W
G

X
H

Putative uncharacterized protein

Uncharacterized protein

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