SMTL ID : 9cdv.1

Crystal Structure of Rhombotarget A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: E.13, V.15, N.17, V.19, E.24, H.48 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.13, A:V.15, A:V.19, A:E.24, A:H.48 MG.2: 2 residues within 4Å: Chain B: D.116, E.152 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.116, B:E.152, H2O.11, H2O.11, H2O.14 MG.3: 6 residues within 4Å: Chain B: E.13, V.15, N.17, V.19, E.24, H.48 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.13, B:V.15, B:V.19, B:E.24, B:H.48

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 12 residues within 4Å: Chain A: R.72, T.108, D.109, K.141, V.142, L.143 Chain B: F.177, Q.210, D.237, S.238, F.239, D.240 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.237, A:R.72, A:R.72, A:D.109, A:K.141, A:L.143 Salt bridges: B:D.237, A:D.109 Water bridges: A:D.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rettie, S.A. et al., Accurate de novo design of high-affinity protein-binding macrocycles using deep learning. Nat.Chem.Biol. (2025)

Release Date

2025-07-02

Peptides

Rhombotarget A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Rhombotarget A

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