SMTL ID : 6ne2.1

Designed repeat protein in complex with Fz7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

ACT.1: 2 residues within 4Å: Chain A: H.83 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.83 ACT.2: 7 residues within 4Å: Chain A: F.80, L.105, H.109, A.110, D.113, F.143 Chain B: K.46 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.113, A:F.143 ACT.3: 7 residues within 4Å: Chain A: S.72, D.76, A.77, F.80 Chain B: H.39, Y.42, P.43 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.80 Hydrogen bonds: A:S.72 Water bridges: A:S.72, A:N.101, B:Q.40 Salt bridges: B:H.39 ACT.4: 2 residues within 4Å: Chain A: D.30, N.32 No protein-ligand interaction detected (PLIP) ACT.5: 4 residues within 4Å: Chain A: A.95, D.96, V.97, N.98 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.97 Hydrogen bonds: A:V.97, A:N.98, A:N.98 ACT.14: 4 residues within 4Å: Chain A: R.147 Chain B: Y.42, K.46, R.54 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.42 Hydrogen bonds: B:Y.42, B:Y.42 Salt bridges: B:K.46, B:R.54 ACT.15: 1 residues within 4Å: Chain B: R.76 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.76 Salt bridges: B:R.76 ACT.16: 4 residues within 4Å: Chain B: R.76, S.77, E.80, V.108 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.109 ACT.17: 1 residues within 4Å: Chain B: R.81 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.81

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

SO4.6: 4 residues within 4Å: Chain A: G.49, H.50, K.51, E.52 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.51, A:E.52 Water bridges: A:G.49, A:H.50, A:V.53 SO4.7: 4 residues within 4Å: Chain A: G.148, H.149, K.150, E.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.150, A:E.151 SO4.8: 5 residues within 4Å: Chain A: G.115, H.116, K.117, E.118 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.117, A:E.118 SO4.9: 5 residues within 4Å: Chain A: H.83, K.84, E.85, V.86 Ligands: ACT.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.83, A:K.84, A:E.85, A:V.86 Salt bridges: A:H.83 SO4.10: 6 residues within 4Å: Chain A: G.82, H.116, K.117, E.118, V.119 Ligands: SO4.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.118, A:V.119 Water bridges: A:K.84, A:G.115, A:H.116 Salt bridges: A:H.116 SO4.18: 4 residues within 4Å: Chain B: R.83, R.102, C.103, E.104 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.103, B:E.104 Water bridges: B:R.83 Salt bridges: B:R.83, B:R.102 SO4.19: 8 residues within 4Å: Chain B: C.75, S.77, L.78, R.81, G.117, Q.118, H.119, H.120 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.78, B:Q.118, B:H.119, B:H.120 Water bridges: B:R.81 Salt bridges: B:R.81, B:H.119, B:H.120 SO4.20: 3 residues within 4Å: Chain A: F.80 Chain B: P.10, H.39 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.42 Salt bridges: B:H.39 SO4.21: 2 residues within 4Å: Chain B: Q.48, R.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.48 Water bridges: B:P.51 Salt bridges: B:R.54 SO4.22: 3 residues within 4Å: Chain B: Q.5, S.8, Q.31 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.8, B:S.8 Water bridges: B:Q.5, B:Q.5, B:Q.31, B:Q.31

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

EDO.11: 5 residues within 4Å: Chain A: Q.67, V.100, N.101 Chain B: F.93, F.95 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.67, A:Q.67, B:F.93 EDO.12: 3 residues within 4Å: Chain A: D.169, A.171, D.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.175

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 1 residues within 4Å: Chain B: N.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.18 Water bridges: B:N.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dang, L.T. et al., Receptor subtype discrimination using extensive shape complementary designed interfaces. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-05-15

Peptides

Designed repeat protein binder: A
Frizzled-7: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Designed repeat protein binder

Frizzled-7

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