SMTL ID : 8ams.1

Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-1-mer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: N.9, L.12, S.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.9, A:S.13 GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.3: 1 residues within 4Å: Chain B: N.83 No protein-ligand interaction detected (PLIP) GOL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.5: 3 residues within 4Å: Chain B: R.138, R.141, E.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.141, B:E.142 GOL.6: 1 residues within 4Å: Chain B: H.57 No protein-ligand interaction detected (PLIP) GOL.9: 4 residues within 4Å: Chain C: Y.26, K.27, N.28, M.83 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.28 GOL.10: 4 residues within 4Å: Chain C: P.66, A.72, L.73, Q.74 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.72, C:Q.74 GOL.14: 2 residues within 4Å: Chain D: L.86, Q.87 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain C: C.34, H.36, C.56, C.59 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.34, C:H.36, C:C.56, C:C.59 ZN.8: 4 residues within 4Å: Chain C: C.19, C.22, C.39, C.42 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.19, C:C.22, C:C.39, C:C.42 ZN.11: 4 residues within 4Å: Chain D: C.34, H.36, C.56, C.59 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.34, D:H.36, D:C.56, D:C.59 ZN.12: 4 residues within 4Å: Chain D: C.19, C.22, C.39, C.42 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.19, D:C.22, D:C.39, D:C.42

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.13: 5 residues within 4Å: Chain C: R.60, T.62 Chain D: T.62, S.63, I.64 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.62, C:T.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Borrajero, C. et al., Structural and biophysical studies of TRIM2 and TRIM3. To Be Published

Release Date

2023-11-15

Peptides

Ubiquitin-conjugating enzyme E2 D3: AB
Tripartite motif-containing protein 2: CD
Polyubiquitin-C: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Ubiquitin-conjugating enzyme E2 D3

Tripartite motif-containing protein 2

Polyubiquitin-C