SMTL ID : 8t09.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x XHZ: 6-ethynyl-2-hydroxynaphthalene-1-carbaldehyde(Covalent)

XHZ.1: 12 residues within 4Å: Chain A: W.46, S.53, L.54, Q.55, K.57, V.94, R.95, A.220, F.222, K.302, L.303, K.306 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.46, A:A.220, A:F.222, A:K.302, A:L.303 Hydrogen bonds: A:K.57, A:K.306 Water bridges: A:R.95

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

GNP.3: 23 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, Y.32, P.34, T.35, G.60, N.116, K.117, D.119, L.120, S.147, A.148, K.149 Ligands: MG.2 24 PLIP interactions: 24 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:G.60, B:N.116, B:K.117, B:K.117, B:A.148, B:K.149 Water bridges: B:D.33, 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

2023-12-13

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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