4NNJ
Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004839 | molecular_function | ubiquitin activating enzyme activity |
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 |
C | 0004839 | molecular_function | ubiquitin activating enzyme activity |
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 |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SO4 A 1101 |
Chain | Residue |
A | ARG21 |
A | HOH1602 |
B | AMP101 |
A | ASN478 |
A | ARG481 |
A | ASP544 |
A | HOH1206 |
A | HOH1256 |
A | HOH1260 |
A | HOH1310 |
A | HOH1447 |
site_id | AC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL A 1102 |
Chain | Residue |
A | GLU155 |
A | ASN162 |
A | LEU273 |
A | HIS293 |
A | PHE296 |
A | GLN297 |
A | HIS300 |
A | TYR390 |
A | HOH1434 |
site_id | AC3 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL A 1103 |
Chain | Residue |
A | ASP282 |
A | LYS285 |
A | PHE391 |
A | ASP392 |
A | SER393 |
A | GLU395 |
A | PHE908 |
A | HOH1277 |
A | HOH1283 |
A | HOH1303 |
site_id | AC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL A 1104 |
Chain | Residue |
A | ARG150 |
A | PHE171 |
A | THR172 |
site_id | AC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL A 1105 |
Chain | Residue |
A | ASN514 |
A | PHE532 |
A | HOH1306 |
site_id | AC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL A 1106 |
Chain | Residue |
A | ASN344 |
A | HOH1649 |
site_id | AC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL A 1107 |
Chain | Residue |
A | ASN828 |
A | HIS830 |
A | HOH1344 |
site_id | AC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL A 1108 |
Chain | Residue |
A | GLU534 |
A | PHE558 |
A | TYR559 |
A | ARG560 |
A | ARG930 |
A | ASP932 |
A | THR1021 |
A | HIS1023 |
site_id | AC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL A 1109 |
Chain | Residue |
A | TYR24 |
A | LYS854 |
site_id | BC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL A 1110 |
Chain | Residue |
A | LYS349 |
A | GLU350 |
A | TYR353 |
A | PRO400 |
A | ARG405 |
site_id | BC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL A 1111 |
Chain | Residue |
A | HIS300 |
A | GLY308 |
site_id | BC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL A 1112 |
Chain | Residue |
A | ASP851 |
A | ARG852 |
A | GLN853 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL A 1113 |
Chain | Residue |
A | GLU29 |
A | LYS33 |
A | THR36 |
C | LYS33 |
site_id | BC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL A 1114 |
Chain | Residue |
A | GLU500 |
A | CYS503 |
A | GLY511 |
A | LYS512 |
A | ILE513 |
A | HOH1590 |
site_id | BC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL A 1116 |
Chain | Residue |
A | ILE1002 |
A | GLU1004 |
A | PHE1019 |
A | HOH1467 |
site_id | BC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL A 1117 |
Chain | Residue |
A | LEU114 |
A | VAL117 |
A | ASP136 |
A | LYS139 |
A | HOH1432 |
A | HOH1437 |
C | TYR723 |
site_id | BC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL A 1118 |
Chain | Residue |
A | ASP721 |
C | GLU142 |
site_id | BC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 A 1119 |
Chain | Residue |
A | GLY27 |
A | LYS28 |
A | GLU29 |
site_id | CC1 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE AMP B 101 |
Chain | Residue |
A | ASN545 |
A | ALA548 |
A | SO41101 |
A | HOH1213 |
A | HOH1260 |
A | HOH1340 |
B | GLY76 |
A | GLY443 |
A | ALA444 |
A | ASP470 |
A | ASP472 |
A | ARG481 |
A | GLN482 |
A | LYS494 |
A | LYS519 |
A | VAL520 |
A | ALA542 |
A | LEU543 |
A | ASP544 |
site_id | CC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 C 1101 |
Chain | Residue |
C | ARG21 |
C | ARG481 |
C | HOH1219 |
C | HOH1235 |
C | HOH1369 |
C | HOH1447 |
C | HOH1514 |
D | AMP101 |
site_id | CC3 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL C 1102 |
Chain | Residue |
C | ASP282 |
C | LYS285 |
C | ASP392 |
C | SER393 |
C | GLU395 |
C | PHE908 |
C | HOH1286 |
C | HOH1287 |
C | HOH1304 |
site_id | CC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL C 1103 |
Chain | Residue |
C | GLU155 |
C | LEU273 |
C | HIS293 |
C | PHE296 |
C | GLN297 |
C | HIS300 |
C | TYR390 |
site_id | CC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL C 1104 |
Chain | Residue |
A | SER940 |
A | ASP941 |
A | GLU944 |
C | THR955 |
C | ASP1008 |
C | GLY1012 |
C | HOH1366 |
C | HOH1640 |
site_id | CC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL C 1105 |
Chain | Residue |
C | LEU737 |
C | ASN828 |
C | HIS830 |
C | HOH1313 |
site_id | CC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL C 1106 |
Chain | Residue |
C | ALA284 |
C | ASP287 |
C | ARG288 |
C | ASN344 |
C | ASP346 |
site_id | CC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL C 1107 |
Chain | Residue |
C | GLY27 |
C | GLY178 |
C | LYS381 |
C | GOL1108 |
site_id | CC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL C 1108 |
Chain | Residue |
C | GLY27 |
C | LYS28 |
C | GLU29 |
C | GOL1107 |
site_id | DC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL C 1109 |
Chain | Residue |
C | GLU534 |
C | PHE558 |
C | ARG560 |
C | ARG930 |
C | ASP932 |
C | THR1021 |
C | HIS1023 |
site_id | DC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL C 1110 |
Chain | Residue |
C | LEU134 |
C | VAL138 |
C | LYS270 |
C | HOH1357 |
C | HOH1602 |
site_id | DC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL C 1111 |
Chain | Residue |
C | ASP472 |
C | ASP544 |
D | AMP101 |
site_id | DC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL C 1112 |
Chain | Residue |
A | TYR723 |
C | LEU114 |
C | VAL117 |
C | ASP136 |
C | HOH1322 |
site_id | DC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL C 1113 |
Chain | Residue |
C | ARG150 |
C | PHE171 |
C | THR172 |
site_id | DC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 C 1114 |
Chain | Residue |
C | ARG202 |
E | ARG42 |
site_id | DC7 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE AMP D 101 |
Chain | Residue |
C | GLY443 |
C | ALA444 |
C | ASP470 |
C | ASP472 |
C | ARG481 |
C | GLN482 |
C | LYS494 |
C | LYS519 |
C | VAL520 |
C | ALA542 |
C | LEU543 |
C | ASP544 |
C | ASN545 |
C | ALA548 |
C | SO41101 |
C | GOL1111 |
C | HOH1201 |
C | HOH1216 |
C | HOH1273 |
C | HOH1369 |
C | HOH1447 |
D | GLY76 |
Functional Information from PROSITE/UniProt
site_id | PS00299 |
Number of Residues | 26 |
Details | UBIQUITIN_1 Ubiquitin domain signature. KskIqDkegIPpdqQrLIFaGkqleD |
Chain | Residue | Details |
B | LYS27-ASP52 |
site_id | PS00536 |
Number of Residues | 9 |
Details | UBIQUITIN_ACTIVAT_1 Ubiquitin-activating enzyme signature 1. KACSGKFtP |
Chain | Residue | Details |
A | LYS376-PRO384 |
site_id | PS00865 |
Number of Residues | 9 |
Details | UBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PLCTLRsFP |
Chain | Residue | Details |
A | PRO598-PRO606 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 18 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0CG47 |
Chain | Residue | Details |
B | LYS6 | |
D | LYS29 | |
D | LYS33 | |
D | LYS63 | |
E | LYS6 | |
E | LYS11 | |
E | LYS27 | |
E | LYS29 | |
E | LYS33 | |
E | LYS63 | |
B | LYS11 | |
B | LYS27 | |
B | LYS29 | |
B | LYS33 | |
B | LYS63 | |
D | LYS6 | |
D | LYS11 | |
D | LYS27 |
site_id | SWS_FT_FI2 |
Number of Residues | 6 |
Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) => ECO:0000255|PROSITE-ProRule:PRU00214 |
Chain | Residue | Details |
A | ALA444 | |
C | ASP544 | |
B | GLY76 | |
A | ARG481 | |
D | GLY76 | |
A | ASP544 | |
E | GLY76 | |
C | ASP470 | |
C | ARG481 | |
C | LYS494 |
site_id | SWS_FT_FI3 |
Number of Residues | 3 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:7862120 |
Chain | Residue | Details |
B | LYS48 | |
D | LYS48 | |
E | LYS48 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956 |
Chain | Residue | Details |
A | SER914 | |
C | SER914 |
site_id | SWS_FT_FI5 |
Number of Residues | 6 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047 |
Chain | Residue | Details |
A | LYS595 | |
A | LYS608 | |
C | LYS595 | |
C | LYS608 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 8 |
Details | M-CSA 307 |
Chain | Residue | Details |
A | ARG21 | electrostatic stabiliser, hydrogen bond donor, steric role |
A | ARG481 | electrostatic stabiliser, hydrogen bond donor, steric role |
A | ASP544 | steric role |
A | CYS600 | activator, covalently attached, hydrogen bond donor, nucleophile, proton donor |
A | THR601 | hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay |
A | ARG603 | electrostatic stabiliser, hydrogen bond donor |
A | ASN781 | electrostatic stabiliser, hydrogen bond donor |
A | ASP782 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA2 |
Number of Residues | 5 |
Details | M-CSA 939 |
Chain | Residue | Details |
A | CYS600 | nucleofuge |
A | THR601 | modifies pKa |
A | ARG603 | electrostatic stabiliser |
A | ASN781 | electrostatic stabiliser |
A | ASP782 | electrostatic stabiliser |
site_id | MCSA3 |
Number of Residues | 8 |
Details | M-CSA 307 |
Chain | Residue | Details |
C | ARG21 | electrostatic stabiliser, hydrogen bond donor, steric role |
C | ARG481 | electrostatic stabiliser, hydrogen bond donor, steric role |
C | ASP544 | steric role |
C | CYS600 | activator, covalently attached, hydrogen bond donor, nucleophile, proton donor |
C | THR601 | hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay |
C | ARG603 | electrostatic stabiliser, hydrogen bond donor |
C | ASN781 | electrostatic stabiliser, hydrogen bond donor |
C | ASP782 | electrostatic stabiliser, hydrogen bond donor |
site_id | MCSA4 |
Number of Residues | 5 |
Details | M-CSA 939 |
Chain | Residue | Details |
C | CYS600 | nucleofuge |
C | THR601 | modifies pKa |
C | ARG603 | electrostatic stabiliser |
C | ASN781 | electrostatic stabiliser |
C | ASP782 | electrostatic stabiliser |