7K5J
Structure of an E1-E2-ubiquitin thioester mimetic
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| A | 0006974 | biological_process | DNA damage response |
| A | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| A | 0016567 | biological_process | protein ubiquitination |
| A | 0016874 | molecular_function | ligase activity |
| A | 0036211 | biological_process | protein modification process |
| A | 0046872 | molecular_function | metal ion binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| C | 0006974 | biological_process | DNA damage response |
| C | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| C | 0016567 | biological_process | protein ubiquitination |
| C | 0016874 | molecular_function | ligase activity |
| C | 0036211 | biological_process | protein modification process |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| D | 0006974 | biological_process | DNA damage response |
| D | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| D | 0016567 | biological_process | protein ubiquitination |
| D | 0016874 | molecular_function | ligase activity |
| D | 0036211 | biological_process | protein modification process |
| D | 0046872 | molecular_function | metal ion binding |
| G | 0000166 | molecular_function | nucleotide binding |
| G | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| G | 0005515 | molecular_function | protein binding |
| G | 0005524 | molecular_function | ATP binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| G | 0006974 | biological_process | DNA damage response |
| G | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| G | 0016567 | biological_process | protein ubiquitination |
| G | 0016874 | molecular_function | ligase activity |
| G | 0036211 | biological_process | protein modification process |
| G | 0046872 | molecular_function | metal ion binding |
| I | 0000166 | molecular_function | nucleotide binding |
| I | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| I | 0005515 | molecular_function | protein binding |
| I | 0005524 | molecular_function | ATP binding |
| I | 0005634 | cellular_component | nucleus |
| I | 0005737 | cellular_component | cytoplasm |
| I | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| I | 0006974 | biological_process | DNA damage response |
| I | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| I | 0016567 | biological_process | protein ubiquitination |
| I | 0016874 | molecular_function | ligase activity |
| I | 0036211 | biological_process | protein modification process |
| I | 0046872 | molecular_function | metal ion binding |
| K | 0000166 | molecular_function | nucleotide binding |
| K | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| K | 0005515 | molecular_function | protein binding |
| K | 0005524 | molecular_function | ATP binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0005737 | cellular_component | cytoplasm |
| K | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| K | 0006974 | biological_process | DNA damage response |
| K | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| K | 0016567 | biological_process | protein ubiquitination |
| K | 0016874 | molecular_function | ligase activity |
| K | 0036211 | biological_process | protein modification process |
| K | 0046872 | molecular_function | metal ion binding |
| M | 0003729 | molecular_function | mRNA binding |
| M | 0005634 | cellular_component | nucleus |
| M | 0005737 | cellular_component | cytoplasm |
| N | 0003729 | molecular_function | mRNA binding |
| N | 0005634 | cellular_component | nucleus |
| N | 0005737 | cellular_component | cytoplasm |
| O | 0003729 | molecular_function | mRNA binding |
| O | 0005634 | cellular_component | nucleus |
| O | 0005737 | cellular_component | cytoplasm |
| P | 0003729 | molecular_function | mRNA binding |
| P | 0005634 | cellular_component | nucleus |
| P | 0005737 | cellular_component | cytoplasm |
| Q | 0003729 | molecular_function | mRNA binding |
| Q | 0005634 | cellular_component | nucleus |
| Q | 0005737 | cellular_component | cytoplasm |
| R | 0003729 | molecular_function | mRNA binding |
| R | 0005634 | cellular_component | nucleus |
| R | 0005737 | cellular_component | cytoplasm |
| S | 0000166 | molecular_function | nucleotide binding |
| S | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| S | 0005515 | molecular_function | protein binding |
| S | 0005524 | molecular_function | ATP binding |
| S | 0005634 | cellular_component | nucleus |
| S | 0005737 | cellular_component | cytoplasm |
| S | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| S | 0006974 | biological_process | DNA damage response |
| S | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| S | 0016567 | biological_process | protein ubiquitination |
| S | 0016874 | molecular_function | ligase activity |
| S | 0036211 | biological_process | protein modification process |
| S | 0046872 | molecular_function | metal ion binding |
| U | 0000166 | molecular_function | nucleotide binding |
| U | 0004839 | molecular_function | ubiquitin activating enzyme activity |
| U | 0005515 | molecular_function | protein binding |
| U | 0005524 | molecular_function | ATP binding |
| U | 0005634 | cellular_component | nucleus |
| U | 0005737 | cellular_component | cytoplasm |
| U | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| U | 0006974 | biological_process | DNA damage response |
| U | 0008641 | molecular_function | ubiquitin-like modifier activating enzyme activity |
| U | 0016567 | biological_process | protein ubiquitination |
| U | 0016874 | molecular_function | ligase activity |
| U | 0036211 | biological_process | protein modification process |
| U | 0046872 | molecular_function | metal ion binding |
| W | 0003729 | molecular_function | mRNA binding |
| W | 0005634 | cellular_component | nucleus |
| W | 0005737 | cellular_component | cytoplasm |
| X | 0003729 | molecular_function | mRNA binding |
| X | 0005634 | cellular_component | nucleus |
| X | 0005737 | cellular_component | cytoplasm |
Functional Information from PROSITE/UniProt
| site_id | PS00183 |
| Number of Residues | 16 |
| Details | UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNVyrd.GrLCIsiL |
| Chain | Residue | Details |
| F | TYR84-LEU99 |
| site_id | PS00536 |
| Number of Residues | 9 |
| Details | UBIQUITIN_ACTIVAT_1 Ubiquitin-activating enzyme signature 1. KACSGKFtP |
| Chain | Residue | Details |
| D | LYS376-PRO384 |
| site_id | PS00865 |
| Number of Residues | 9 |
| Details | UBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PLCTLRsFP |
| Chain | Residue | Details |
| D | PRO598-PRO606 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 300 |
| Details | Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1096 |
| Details | Repeat: {"description":"1-1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1232 |
| Details | Repeat: {"description":"1-2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4416 |
| Details | Region: {"description":"2 approximate repeats"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10132","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 56 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 40 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 16 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 6 |
| Details | Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| B | LEU12 | electrostatic stabiliser, hydrogen bond donor, steric role |
| site_id | MCSA10 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| site_id | MCSA11 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| L | LEU12 | electrostatic stabiliser, hydrogen bond donor, steric role |
| site_id | MCSA12 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| site_id | MCSA13 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| S | ARG21 | electrostatic stabiliser, hydrogen bond donor, steric role |
| S | ARG481 | electrostatic stabiliser, hydrogen bond donor, steric role |
| S | ASP544 | steric role |
| S | CYS600 | activator, covalently attached, hydrogen bond donor, nucleophile, proton donor |
| S | THR601 | hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay |
| S | ARG603 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA14 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| S | CYS600 | nucleofuge |
| S | THR601 | modifies pKa |
| S | ARG603 | electrostatic stabiliser |
| site_id | MCSA15 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| U | ARG21 | electrostatic stabiliser, hydrogen bond donor, steric role |
| U | ARG481 | electrostatic stabiliser, hydrogen bond donor, steric role |
| U | ASP544 | steric role |
| U | CYS600 | activator, covalently attached, hydrogen bond donor, nucleophile, proton donor |
| U | THR601 | hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay |
| U | ARG603 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA16 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| U | CYS600 | nucleofuge |
| U | THR601 | modifies pKa |
| U | ARG603 | electrostatic stabiliser |
| site_id | MCSA2 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| D | ARG21 | electrostatic stabiliser, hydrogen bond donor, steric role |
| D | ARG481 | electrostatic stabiliser, hydrogen bond donor, steric role |
| D | ASP544 | steric role |
| D | CYS600 | activator, covalently attached, hydrogen bond donor, nucleophile, proton donor |
| D | THR601 | hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay |
| D | ARG603 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA4 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| D | CYS600 | nucleofuge |
| D | THR601 | modifies pKa |
| D | ARG603 | electrostatic stabiliser |
| site_id | MCSA5 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| F | LEU12 | electrostatic stabiliser, hydrogen bond donor, steric role |
| site_id | MCSA6 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| site_id | MCSA7 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| H | LEU12 | electrostatic stabiliser, hydrogen bond donor, steric role |
| site_id | MCSA8 |
| Number of Residues | 3 |
| Details | M-CSA 939 |
| Chain | Residue | Details |
| site_id | MCSA9 |
| Number of Residues | 6 |
| Details | M-CSA 307 |
| Chain | Residue | Details |
| J | LEU12 | electrostatic stabiliser, hydrogen bond donor, steric role |
