SMTL ID : 8t7v.1

Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-(furan-2-yl)-2-hydroxy-1-naphthaldehyde)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZTA: (7M)-7-(furan-2-yl)-2-hydroxynaphthalene-1-carbaldehyde(Covalent)

ZTA.1: 9 residues within 4Å: Chain A: L.56, Q.57, K.59, V.96, R.97, F.224, K.304, L.305, K.308 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.57, A:V.96, A:R.97, A:F.224, A:K.304, A:L.305 Hydrogen bonds: A:K.59, A:K.308 pi-Cation interactions: A:K.59

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: S.17, T.35, D.57 Ligands: GNP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:T.35, H2O.1, H2O.1

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.3: 25 residues within 4Å: Chain B: S.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, E.30, K.31, Y.32, P.34, T.35, A.59, G.60, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:K.16, B:K.16, B:S.17, B:A.18, B:V.29, B:Y.32, B:Y.32, B:T.35, B:T.58, B:N.116, B:K.117, B:K.117, B:A.148, B:K.149 Water bridges: B:T.35, B:T.35 Salt bridges: B:D.119 pi-Stacking: B:F.28, B:F.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Francisco, K.R. et al., Targeted Reversible Covalent Modification of a Noncatalytic Lysine of the Krev Interaction Trapped 1 Protein Enables Site-Directed Screening for Protein-Protein Interaction Inhibitors. Acs Pharmacol Transl Sci (2023)

Release Date

2023-12-06

Peptides

Krev interaction trapped protein 1: A
Ras-related protein Rap-1b: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Krev interaction trapped protein 1

Ras-related protein Rap-1b

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