SMTL ID : 9gte.1

Crystal structure of TRIM21 PRY-SPRY domain bound to Suramin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: Q.72, G.175, G.176, N.177, A.178, A.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.175, A:A.178, A:A.179 Water bridges: A:N.172 EDO.2: 4 residues within 4Å: Chain A: D.14, A.56, R.58, R.164 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: Y.134, V.158, F.159, A.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.159, A:A.160 EDO.4: 7 residues within 4Å: Chain A: Y.50, M.52, D.77, F.91, S.92, L.93, N.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.91, A:L.93, A:N.168 EDO.5: 7 residues within 4Å: Chain A: N.19, M.33, S.48, N.49, Y.50, P.51, F.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19 EDO.6: 3 residues within 4Å: Chain A: F.131, Y.142 Ligands: SVR.7 No protein-ligand interaction detected (PLIP)

1 x SVR: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID(Non-covalent)

SVR.7: 19 residues within 4Å: Chain A: H.3, H.4, H.5, H.6, H.7, K.63, Y.65, E.67, V.68, D.69, Q.127, F.131, Y.142, I.144, K.182, L.183, C.184, P.185 Ligands: EDO.6 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:H.7, A:K.63, A:K.63, A:Y.65, A:Y.65, A:E.67, A:D.69, A:Q.127, A:F.131, A:Y.142, A:K.182, A:P.185 Hydrogen bonds: A:H.5, A:H.6, A:H.7, A:H.7, A:Y.65, A:E.67, A:E.67 Water bridges: A:Q.30, A:K.63, A:K.63, A:K.63, A:K.63, A:E.67, A:E.67 Salt bridges: A:H.4, A:H.5, A:H.6, A:K.63, A:K.63 pi-Stacking: A:Y.65 pi-Cation interactions: A:K.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal structure of TRIM21 PRY-SPRY domain bound to Suramin. To Be Published

Release Date

2024-10-30

Peptides

E3 ubiquitin-protein ligase TRIM21: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E3 ubiquitin-protein ligase TRIM21

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