SMTL ID : 6sqr.1

Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-4-3-2-1-1-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: N.11, E.14, V.17, K.24 Chain C: T.10, K.12 Chain D: P.64 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:P.64, A:N.11, A:E.14, A:K.24 Water bridges: A:E.14, A:P.15 EDO.4: 5 residues within 4Å: Chain A: V.17 Chain B: R.4, A.95, T.97 Chain C: T.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.95 EDO.5: 5 residues within 4Å: Chain D: K.42, N.45, K.46, P.54, I.55 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.46, D:I.55 EDO.6: 1 residues within 4Å: Chain D: N.45 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.45 EDO.10: 6 residues within 4Å: Chain G: N.5, E.8, V.11, K.18 Chain I: T.9 Chain J: P.64 4 PLIP interactions: 1 interactions with chain I, 2 interactions with chain G, 1 interactions with chain J Hydrogen bonds: I:T.9, G:N.5, G:K.18, J:P.64 EDO.11: 4 residues within 4Å: Chain G: N.19, L.59, T.60, Y.61 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.19 Water bridges: G:Y.61 EDO.15: 6 residues within 4Å: Chain H: Q.19, L.103 Chain I: F.45, A.46, G.47, H.68 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:A.46, I:G.47 Water bridges: I:H.68 EDO.17: 6 residues within 4Å: Chain G: E.1, P.3 Chain I: K.11, E.34 Chain J: Y.62, F.63 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G, 1 interactions with chain J Hydrogen bonds: I:K.11, G:E.1, J:F.63 Water bridges: I:E.34 EDO.18: 7 residues within 4Å: Chain G: P.63 Chain J: N.6, E.9, V.12, K.19 Chain L: T.10, K.12 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L, 2 interactions with chain G Hydrogen bonds: J:N.6, J:K.19, L:T.10, G:P.63 Water bridges: G:P.63 EDO.21: 7 residues within 4Å: Chain K: F.68, T.69, T.70, R.71, S.79, N.80, G.81 3 PLIP interactions: 3 interactions with chain K Water bridges: K:T.69, K:I.72, K:N.78 EDO.22: 2 residues within 4Å: Chain K: T.35, F.50 No protein-ligand interaction detected (PLIP) EDO.23: 7 residues within 4Å: Chain J: V.12 Chain K: R.4, K.7, A.95, T.97 Chain L: L.9, T.10 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:A.95 Water bridges: J:Q.15

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.16, C.19, R.22, C.39, C.42 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.16, A:C.19, A:C.39, A:C.42 ZN.3: 4 residues within 4Å: Chain A: H.30, H.35, C.53, C.56 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.30, A:H.35, A:C.53, A:C.56 ZN.8: 4 residues within 4Å: Chain D: C.11, C.14, C.34, C.37 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.11, D:C.14, D:C.34, D:C.37 ZN.9: 4 residues within 4Å: Chain D: H.25, H.30, C.48, C.51 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.25, D:H.30, D:C.48, D:C.51 ZN.12: 5 residues within 4Å: Chain G: C.10, C.13, R.16, C.33, C.36 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.10, G:C.13, G:C.33, G:C.36 ZN.13: 4 residues within 4Å: Chain G: H.24, H.29, C.47, C.50 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.24, G:H.29, G:C.47, G:C.50 ZN.19: 5 residues within 4Å: Chain J: C.11, C.14, R.17, C.34, C.37 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.11, J:C.14, J:C.34, J:C.37 ZN.20: 5 residues within 4Å: Chain J: H.25, H.30, C.48, V.50, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.25, J:H.30, J:C.48, J:C.51

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 2 residues within 4Å: Chain D: C.14, R.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.17, D:R.17 Water bridges: D:C.14, D:T.16 NO3.14: 5 residues within 4Å: Chain G: V.11 Chain H: R.4, A.95, T.97 Chain I: T.9 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:L.8, G:Q.14 NO3.16: 5 residues within 4Å: Chain I: K.27, Q.49, L.50, E.51, D.52 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:K.27, I:Q.49, I:D.52 Water bridges: I:K.27, I:D.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magnussen, H.M. et al., Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. Nat Commun (2020)

Release Date

2020-05-06

Peptides

E3 ubiquitin-protein ligase Mdm2: A
Ubiquitin-conjugating enzyme E2 D2: BEHK
Ubiquitin-40S ribosomal protein S27a: CFL
E3 ubiquitin-protein ligase Mdm2: DJ
E3 ubiquitin-protein ligase Mdm2: G
Polyubiquitin-C: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

H
H

K
K

C
C

F
F

L
L

D
D

J
J

G
G

I
I

E3 ubiquitin-protein ligase Mdm2

Ubiquitin-conjugating enzyme E2 D2

Ubiquitin-40S ribosomal protein S27a

E3 ubiquitin-protein ligase Mdm2

E3 ubiquitin-protein ligase Mdm2

Polyubiquitin-C

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