SMTL ID : 5aiu.1

A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.10, C.13, C.37, C.40 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:C.13, A:C.37, A:C.40 ZN.2: 5 residues within 4Å: Chain A: T.30, C.32, H.34, C.51, C.54 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.32, A:H.34, A:C.51, A:C.54 ZN.3: 4 residues within 4Å: Chain A: C.75, C.78, C.102, C.105 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.75, A:C.78, A:C.102, A:C.105 ZN.4: 5 residues within 4Å: Chain A: T.95, C.97, H.99, C.116, C.119 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:H.99, A:C.116, A:C.119

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

EDO.5: 6 residues within 4Å: Chain A: Y.67, P.76, H.99, V.100, F.101, T.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.67, A:V.100 EDO.6: 10 residues within 4Å: Chain B: F.49, F.54, K.76, I.77, Y.78, A.142, W.145, T.146, Y.149, A.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.78, B:Y.78, B:T.146 EDO.7: 6 residues within 4Å: Chain B: L.17, P.21, V.22, I.25, K.26, A.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.22, B:V.22, B:A.27 EDO.8: 8 residues within 4Å: Chain B: P.23, L.108, Q.111 Chain C: I.44, F.45, A.46, G.47, H.68 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.46, C:G.47, B:Q.111 EDO.9: 10 residues within 4Å: Chain D: F.49, F.54, K.76, I.77, Y.78, A.142, W.145, T.146, Y.149, A.150 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.78, D:Y.78 EDO.10: 7 residues within 4Å: Chain D: P.23, L.108 Chain E: I.44, F.45, A.46, G.47, H.68 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:A.46, E:G.47 Water bridges: D:Q.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Branigan, E. et al., Structural Basis for the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-07-08

Peptides

E3 UBIQUITIN-PROTEIN LIGASE RNF4: A
UBIQUITIN-CONJUGATING ENZYME E2 N: BD
POLYUBIQUITIN-C: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
E

C
C

E
F

E3 UBIQUITIN-PROTEIN LIGASE RNF4

UBIQUITIN-CONJUGATING ENZYME E2 N

POLYUBIQUITIN-C

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