5DC2
X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0008360 | biological_process | regulation of cell shape |
| A | 0009252 | biological_process | peptidoglycan biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016746 | molecular_function | acyltransferase activity |
| A | 0018104 | biological_process | peptidoglycan-protein cross-linking |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0071555 | biological_process | cell wall organization |
| A | 0071972 | molecular_function | peptidoglycan L,D-transpeptidase activity |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0008360 | biological_process | regulation of cell shape |
| B | 0009252 | biological_process | peptidoglycan biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016746 | molecular_function | acyltransferase activity |
| B | 0018104 | biological_process | peptidoglycan-protein cross-linking |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0071555 | biological_process | cell wall organization |
| B | 0071972 | molecular_function | peptidoglycan L,D-transpeptidase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 13 |
| Details | binding site for residue 58U A 501 |
| Chain | Residue |
| A | MET303 |
| A | ASN356 |
| A | EDO516 |
| A | HOH606 |
| A | HOH625 |
| A | TYR318 |
| A | GLY332 |
| A | HIS336 |
| A | TRP340 |
| A | SER351 |
| A | HIS352 |
| A | GLY353 |
| A | CYS354 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 A 502 |
| Chain | Residue |
| A | ARG122 |
| A | SO4506 |
| A | HOH601 |
| A | HOH656 |
| B | PRO311 |
| B | VAL312 |
| B | ASN313 |
| B | HOH641 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 503 |
| Chain | Residue |
| A | ARG371 |
| A | HOH626 |
| A | HOH652 |
| A | HOH695 |
| A | HOH758 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 504 |
| Chain | Residue |
| A | MET157 |
| A | TYR330 |
| A | ARG371 |
| A | HOH605 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 505 |
| Chain | Residue |
| A | SER106 |
| A | PRO107 |
| A | ARG111 |
| A | HOH628 |
| A | HOH703 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 506 |
| Chain | Residue |
| A | ASN95 |
| A | ARG99 |
| A | SO4502 |
| A | HOH601 |
| A | HOH619 |
| B | SER306 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue PEG A 507 |
| Chain | Residue |
| A | ASN204 |
| A | ASN205 |
| A | HOH761 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue PEG A 508 |
| Chain | Residue |
| A | GLY86 |
| A | LEU131 |
| A | GLY132 |
| A | HOH615 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue PEG A 509 |
| Chain | Residue |
| A | GLU185 |
| A | ALA199 |
| A | PHE200 |
| A | TRP401 |
| A | ARG402 |
| A | GLY404 |
| A | PEG510 |
| A | HOH688 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue PEG A 510 |
| Chain | Residue |
| A | ILE188 |
| A | LYS189 |
| A | ILE190 |
| A | GLY198 |
| A | TRP210 |
| A | PEG509 |
| A | HOH750 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue PGE A 511 |
| Chain | Residue |
| A | HIS214 |
| A | PHE215 |
| A | GLU252 |
| A | ILE254 |
| A | HOH638 |
| B | LYS186 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue PGE A 512 |
| Chain | Residue |
| A | LYS189 |
| A | ILE190 |
| A | THR192 |
| A | VAL196 |
| A | HOH719 |
| B | ASN260 |
| site_id | AD4 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 513 |
| Chain | Residue |
| A | ARG123 |
| A | THR142 |
| A | SER358 |
| A | PRO359 |
| A | SER360 |
| A | HOH603 |
| A | HOH714 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 514 |
| Chain | Residue |
| A | ARG181 |
| A | TRP202 |
| A | LEU203 |
| A | HOH608 |
| A | HOH621 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 515 |
| Chain | Residue |
| A | VAL75 |
| A | ALA77 |
| A | PRO78 |
| A | GLN117 |
| A | LEU118 |
| A | HOH763 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 516 |
| Chain | Residue |
| A | TYR318 |
| A | SER331 |
| A | HIS352 |
| A | GLY353 |
| A | 58U501 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 502 |
| Chain | Residue |
| B | ARG371 |
| B | HOH621 |
| B | HOH681 |
| B | ARG297 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 B 503 |
| Chain | Residue |
| A | PRO311 |
| A | VAL312 |
| A | ASN313 |
| B | ARG122 |
| B | SO4504 |
| B | HOH616 |
| B | HOH623 |
| B | HOH749 |
| site_id | AE1 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 B 504 |
| Chain | Residue |
| A | SER306 |
| A | PRO311 |
| B | ASN95 |
| B | ASN97 |
| B | ARG99 |
| B | SO4503 |
| B | HOH658 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 505 |
| Chain | Residue |
| B | ARG104 |
| B | SER106 |
| B | PRO107 |
| B | ARG111 |
| B | HOH630 |
| B | HOH748 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue PEG B 507 |
| Chain | Residue |
| A | LEU62 |
| A | ARG139 |
| A | LEU141 |
| B | ASP399 |
| B | HOH609 |
| B | HOH622 |
| site_id | AE4 |
| Number of Residues | 2 |
| Details | binding site for residue PEG B 508 |
| Chain | Residue |
| B | ILE190 |
| B | TRP210 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue PEG B 509 |
| Chain | Residue |
| A | VAL71 |
| A | HOH843 |
| B | GLU213 |
| B | HIS214 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue PEG B 510 |
| Chain | Residue |
| B | PRO386 |
| B | GLY387 |
| B | GLN400 |
| B | PGE514 |
| B | HOH610 |
| B | HOH613 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue PEG B 511 |
| Chain | Residue |
| B | ASP251 |
| B | HIS368 |
| B | HOH611 |
| B | HOH635 |
| site_id | AE8 |
| Number of Residues | 6 |
| Details | binding site for residue PGE B 512 |
| Chain | Residue |
| B | GLU376 |
| B | VAL378 |
| B | PRO397 |
| B | GOL515 |
| B | HOH603 |
| B | HOH763 |
| site_id | AE9 |
| Number of Residues | 8 |
| Details | binding site for residue PGE B 513 |
| Chain | Residue |
| B | GLU168 |
| B | PRO169 |
| B | ALA171 |
| B | GLY295 |
| B | SER296 |
| B | GLN327 |
| B | TYR330 |
| B | ARG371 |
| site_id | AF1 |
| Number of Residues | 8 |
| Details | binding site for residue PGE B 514 |
| Chain | Residue |
| B | ARG181 |
| B | TYR201 |
| B | TRP202 |
| B | ILE388 |
| B | ASN405 |
| B | ALA408 |
| B | PEG510 |
| B | HOH610 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 515 |
| Chain | Residue |
| B | GLU213 |
| B | HIS214 |
| B | PHE215 |
| B | ILE291 |
| B | PGE512 |
| B | HOH750 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 516 |
| Chain | Residue |
| B | ALA90 |
| B | VAL91 |
| B | LEU105 |
| B | TRP112 |
| site_id | AF4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 517 |
| Chain | Residue |
| B | TYR318 |
| B | SER331 |
| B | GLY332 |
| B | 58U501 |
| site_id | AF5 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide 58U B 501 and CYS B 354 |
| Chain | Residue |
| B | SER279 |
| B | MET280 |
| B | MET303 |
| B | TYR318 |
| B | GLY332 |
| B | PHE334 |
| B | HIS336 |
| B | TRP340 |
| B | SER351 |
| B | HIS352 |
| B | GLY353 |
| B | LEU355 |
| B | ASN356 |
| B | EDO517 |
| B | HOH612 |
| site_id | AF6 |
| Number of Residues | 12 |
| Details | binding site for Di-peptide SO4 B 506 and ARG B 123 |
| Chain | Residue |
| B | ASN95 |
| B | ASP96 |
| B | ARG122 |
| B | TYR124 |
| B | PHE143 |
| B | GLN144 |
| B | SER358 |
| B | SER358 |
| B | SER360 |
| B | HOH605 |
| B | HOH638 |
| B | HOH732 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 250 |
| Details | Domain: {"description":"L,D-TPase catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01373","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01373","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23103390","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01373","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23103390","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Site: {"description":"Binds to carbapenem drug (covalent)","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
