Structure of PDB 7k5j Chain D

Receptor sequence

>7k5jD (length=972) Species: 559292 (Saccharomyces cerevisiae S288C)

GEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVK
SMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVL
DSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFG
NTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNFV
RFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVP
RKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELP
RTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPG
VVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQ
PVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSG
SDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKG
KINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRK
PLLESGTLGTKGNTQVIIPRLTESYSSSRCTLRSFPNKIDHTIAWAKSLF
QGYFTDSAENVNMYLTQPNFVEQTLKDVKGVLESISDSLSSKPHNFEDCI
KWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIY
NNDHFHFVVAGASLRAYNYGIKKPNVDEYKSVIDHMIIPEFTPNEIDQLV
SSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADR
QKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLA
LPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGL
EITMLSYGVSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMI
LEICADDKEGEDVEVPFITIHL

3D structure

• PDB: 7k5j Crystal structures of an E1-E2-ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification.
• Chain: D
• Resolution: 3.42 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R21 R481 D544 C600 T601 R603
• Catalytic site (residue number reindexed from 1): R10 R470 D533 C580 T581 R583
• Enzyme Commision number: 6.2.1.45: E1 ubiquitin-activating enzyme.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	AMP	D	G443 A444 D470 N471 D472 K494 K519 V520 L543 D544 N545	G432 A433 D459 N460 D461 K483 K508 V509 L532 D533 N534

Gene Ontology

Molecular Function

• GO:0004839 ubiquitin activating enzyme activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008641 ubiquitin-like modifier activating enzyme activity
• GO:0016874 ligase activity

Biological Process

• GO:0006511 ubiquitin-dependent protein catabolic process
• GO:0006974 DNA damage response
• GO:0016567 protein ubiquitination
• GO:0036211 protein modification process
• GO:0043412 macromolecule modification

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm

External links

• PDB: RCSB:7k5j, PDBe:7k5j, PDBj:7k5j
• PDBsum: 7k5j
• PubMed: 33888705
• UniProt: P22515|UBA1_YEAST Ubiquitin-activating enzyme E1 1 (Gene Name=UBA1)