SMTL ID : 3kyd.1

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: F.159, G.163, Y.164, D.239, L.242, L.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.239 Water bridges: A:G.163 EDO.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: R.235 Chain B: R.427 Chain C: E.86 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Water bridges: B:K.429, A:R.235, A:R.235 Hydrogen bonds: C:E.86

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.160, C.163, C.443, C.446 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.160, B:C.163, B:C.443, B:C.446

1 x VMX: 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine(Covalent)

VMX.4: 21 residues within 4Å: Chain B: G.26, G.28, G.29, I.30, D.50, L.51, D.52, K.74, D.96, S.97, I.98, A.117, L.118, D.119, N.120, A.123, T.143, C.175, T.176, R.178 Chain C: G.115 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.29, B:I.30, B:L.51, B:D.52, B:K.74, B:S.97, B:I.98, B:A.117, B:N.120, B:T.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olsen, S.K. et al., Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature (2010)

Release Date

2010-02-16

Peptides

SUMO-activating enzyme subunit 1: A
SUMO-activating enzyme subunit 2: B
Small ubiquitin-related modifier 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

SUMO-activating enzyme subunit 1

SUMO-activating enzyme subunit 2

Small ubiquitin-related modifier 1

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