5VXO
Crystal Structure Analysis of human CLYBL in complex with propionyl-CoA
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000287 | molecular_function | magnesium ion binding |
A | 0003824 | molecular_function | catalytic activity |
A | 0004474 | molecular_function | malate synthase activity |
A | 0005739 | cellular_component | mitochondrion |
A | 0016740 | molecular_function | transferase activity |
A | 0016787 | molecular_function | hydrolase activity |
A | 0016829 | molecular_function | lyase activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0047777 | molecular_function | (S)-citramalyl-CoA lyase activity |
A | 0070207 | biological_process | protein homotrimerization |
A | 0106064 | biological_process | regulation of cobalamin metabolic process |
A | 0106121 | biological_process | positive regulation of cobalamin metabolic process |
B | 0000287 | molecular_function | magnesium ion binding |
B | 0003824 | molecular_function | catalytic activity |
B | 0004474 | molecular_function | malate synthase activity |
B | 0005739 | cellular_component | mitochondrion |
B | 0016740 | molecular_function | transferase activity |
B | 0016787 | molecular_function | hydrolase activity |
B | 0016829 | molecular_function | lyase activity |
B | 0046872 | molecular_function | metal ion binding |
B | 0047777 | molecular_function | (S)-citramalyl-CoA lyase activity |
B | 0070207 | biological_process | protein homotrimerization |
B | 0106064 | biological_process | regulation of cobalamin metabolic process |
B | 0106121 | biological_process | positive regulation of cobalamin metabolic process |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0003824 | molecular_function | catalytic activity |
C | 0004474 | molecular_function | malate synthase activity |
C | 0005739 | cellular_component | mitochondrion |
C | 0016740 | molecular_function | transferase activity |
C | 0016787 | molecular_function | hydrolase activity |
C | 0016829 | molecular_function | lyase activity |
C | 0046872 | molecular_function | metal ion binding |
C | 0047777 | molecular_function | (S)-citramalyl-CoA lyase activity |
C | 0070207 | biological_process | protein homotrimerization |
C | 0106064 | biological_process | regulation of cobalamin metabolic process |
C | 0106121 | biological_process | positive regulation of cobalamin metabolic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 20 |
Details | binding site for residue 1VU A 501 |
Chain | Residue |
A | TYR50 |
A | ILE272 |
A | HIS273 |
A | PRO274 |
A | HOH604 |
A | HOH646 |
A | HOH647 |
A | HOH657 |
A | HOH658 |
B | THR313 |
B | MET318 |
A | VAL51 |
B | ASP320 |
A | LYS57 |
A | LYS58 |
A | LYS61 |
A | ASP76 |
A | GLY77 |
A | ARG107 |
A | ARG249 |
site_id | AC2 |
Number of Residues | 8 |
Details | binding site for residue EDO A 502 |
Chain | Residue |
A | GLY212 |
A | ALA213 |
A | THR214 |
B | ALA262 |
B | ALA263 |
B | LYS290 |
B | EDO503 |
B | EDO507 |
site_id | AC3 |
Number of Residues | 7 |
Details | binding site for residue EDO A 503 |
Chain | Residue |
A | VAL78 |
A | ALA79 |
A | ALA80 |
A | LYS83 |
A | HOH625 |
B | GLN305 |
B | MET321 |
site_id | AC4 |
Number of Residues | 5 |
Details | binding site for residue EDO A 504 |
Chain | Residue |
A | ILE97 |
A | ASP98 |
A | LEU99 |
A | LYS104 |
A | HOH630 |
site_id | AC5 |
Number of Residues | 2 |
Details | binding site for residue EDO A 505 |
Chain | Residue |
A | LYS325 |
C | ASP206 |
site_id | AC6 |
Number of Residues | 4 |
Details | binding site for residue EDO A 506 |
Chain | Residue |
A | ASP198 |
A | GLY237 |
A | GLN239 |
A | HOH629 |
site_id | AC7 |
Number of Residues | 4 |
Details | binding site for residue EDO A 507 |
Chain | Residue |
A | ASP76 |
A | LYS137 |
B | MET321 |
B | LYS325 |
site_id | AC8 |
Number of Residues | 1 |
Details | binding site for residue EDO A 508 |
Chain | Residue |
A | ASP68 |
site_id | AC9 |
Number of Residues | 4 |
Details | binding site for residue EDO A 509 |
Chain | Residue |
A | LYS228 |
A | HOH660 |
B | HOH601 |
C | EDO503 |
site_id | AD1 |
Number of Residues | 5 |
Details | binding site for residue EDO A 510 |
Chain | Residue |
A | GLU56 |
A | ARG89 |
A | LYS92 |
A | THR93 |
A | ILE97 |
site_id | AD2 |
Number of Residues | 3 |
Details | binding site for residue EDO A 511 |
Chain | Residue |
A | GLN125 |
A | HIS154 |
A | LYS156 |
site_id | AD3 |
Number of Residues | 1 |
Details | binding site for residue EDO A 512 |
Chain | Residue |
A | LYS82 |
site_id | AD4 |
Number of Residues | 4 |
Details | binding site for residue PEG A 513 |
Chain | Residue |
A | ALA334 |
A | THR335 |
A | SER336 |
A | ILE337 |
site_id | AD5 |
Number of Residues | 1 |
Details | binding site for residue PEG A 514 |
Chain | Residue |
A | VAL111 |
site_id | AD6 |
Number of Residues | 6 |
Details | binding site for residue PEG A 515 |
Chain | Residue |
A | GLU95 |
A | ASP96 |
A | ARG127 |
B | GLU121 |
B | GLN125 |
B | LYS156 |
site_id | AD7 |
Number of Residues | 3 |
Details | binding site for residue PGE A 516 |
Chain | Residue |
A | GLU117 |
A | LYS150 |
A | PHE153 |
site_id | AD8 |
Number of Residues | 6 |
Details | binding site for residue PG4 A 517 |
Chain | Residue |
A | TYR42 |
A | LYS234 |
A | GLY237 |
A | LEU238 |
A | HOH617 |
A | HOH699 |
site_id | AD9 |
Number of Residues | 7 |
Details | binding site for residue PG4 A 518 |
Chain | Residue |
A | GLU289 |
A | LYS290 |
A | TRP293 |
A | PHE314 |
A | SER317 |
C | THR214 |
C | SER215 |
site_id | AE1 |
Number of Residues | 9 |
Details | binding site for residue PO4 A 519 |
Chain | Residue |
C | EDO503 |
A | TYR224 |
A | LYS228 |
A | HOH642 |
A | HOH660 |
B | TYR224 |
B | LYS228 |
C | TYR224 |
C | LYS228 |
site_id | AE2 |
Number of Residues | 17 |
Details | binding site for residue 1VU B 501 |
Chain | Residue |
B | TYR50 |
B | LYS57 |
B | LYS58 |
B | LYS61 |
B | GLY77 |
B | ARG107 |
B | ILE272 |
B | HIS273 |
B | PRO274 |
B | HOH605 |
B | HOH607 |
B | HOH658 |
B | HOH667 |
C | ALA311 |
C | THR313 |
C | MET318 |
C | ASP320 |
site_id | AE3 |
Number of Residues | 3 |
Details | binding site for residue EDO B 502 |
Chain | Residue |
B | GLU139 |
B | THR172 |
B | SER210 |
site_id | AE4 |
Number of Residues | 7 |
Details | binding site for residue EDO B 503 |
Chain | Residue |
A | EDO502 |
B | LYS290 |
B | GLN326 |
B | ASN329 |
B | THR330 |
B | EDO507 |
B | HOH622 |
site_id | AE5 |
Number of Residues | 2 |
Details | binding site for residue EDO B 504 |
Chain | Residue |
B | ALA300 |
B | PGE514 |
site_id | AE6 |
Number of Residues | 5 |
Details | binding site for residue EDO B 505 |
Chain | Residue |
B | HIS304 |
B | THR313 |
B | EDO508 |
B | PGE514 |
B | HOH672 |
site_id | AE7 |
Number of Residues | 3 |
Details | binding site for residue EDO B 506 |
Chain | Residue |
B | TYR42 |
B | SER336 |
B | PEG513 |
site_id | AE8 |
Number of Residues | 8 |
Details | binding site for residue EDO B 507 |
Chain | Residue |
A | EDO502 |
B | GLN283 |
B | SER285 |
B | PRO286 |
B | LYS290 |
B | LEU333 |
B | EDO503 |
B | HOH647 |
site_id | AE9 |
Number of Residues | 6 |
Details | binding site for residue EDO B 508 |
Chain | Residue |
B | THR313 |
B | PHE314 |
B | GLN315 |
B | EDO505 |
B | PGE514 |
B | HOH703 |
site_id | AF1 |
Number of Residues | 2 |
Details | binding site for residue EDO B 510 |
Chain | Residue |
B | GLU289 |
B | LYS292 |
site_id | AF2 |
Number of Residues | 3 |
Details | binding site for residue EDO B 511 |
Chain | Residue |
B | ARG158 |
B | LYS159 |
B | HOH628 |
site_id | AF3 |
Number of Residues | 1 |
Details | binding site for residue PEG B 512 |
Chain | Residue |
B | TRP293 |
site_id | AF4 |
Number of Residues | 6 |
Details | binding site for residue PEG B 513 |
Chain | Residue |
A | SER210 |
B | LYS234 |
B | GLY237 |
B | LEU238 |
B | EDO506 |
B | HOH650 |
site_id | AF5 |
Number of Residues | 7 |
Details | binding site for residue PGE B 514 |
Chain | Residue |
B | ALA300 |
B | HIS304 |
B | THR313 |
B | PHE314 |
B | EDO504 |
B | EDO505 |
B | EDO508 |
site_id | AF6 |
Number of Residues | 17 |
Details | binding site for residue 1VU C 501 |
Chain | Residue |
A | ALA311 |
A | MET318 |
A | ASP320 |
C | TYR50 |
C | VAL51 |
C | LYS57 |
C | LYS58 |
C | LYS61 |
C | GLY77 |
C | ARG107 |
C | ILE272 |
C | HIS273 |
C | PRO274 |
C | HOH603 |
C | HOH615 |
C | HOH637 |
C | HOH669 |
site_id | AF7 |
Number of Residues | 3 |
Details | binding site for residue EDO C 502 |
Chain | Residue |
C | VAL111 |
C | GLU142 |
C | TRP146 |
site_id | AF8 |
Number of Residues | 5 |
Details | binding site for residue EDO C 503 |
Chain | Residue |
A | EDO509 |
A | PO4519 |
B | LYS228 |
B | HOH601 |
C | LYS228 |
site_id | AF9 |
Number of Residues | 8 |
Details | binding site for residue EDO C 504 |
Chain | Residue |
C | TYR42 |
C | ASP198 |
C | GLY237 |
C | GLN239 |
C | EDO506 |
C | PGE511 |
C | HOH639 |
C | HOH682 |
site_id | AG1 |
Number of Residues | 3 |
Details | binding site for residue EDO C 505 |
Chain | Residue |
C | HIS304 |
C | PHE312 |
C | THR313 |
site_id | AG2 |
Number of Residues | 5 |
Details | binding site for residue EDO C 506 |
Chain | Residue |
C | HIS40 |
C | TYR42 |
C | EDO504 |
C | PEG510 |
C | PGE511 |
site_id | AG3 |
Number of Residues | 1 |
Details | binding site for residue EDO C 507 |
Chain | Residue |
C | TRP293 |
site_id | AG4 |
Number of Residues | 9 |
Details | binding site for residue EDO C 508 |
Chain | Residue |
C | TYR42 |
C | PRO44 |
C | ARG45 |
C | ARG46 |
C | GLN239 |
C | THR267 |
C | PG4512 |
C | HOH651 |
C | HOH672 |
site_id | AG5 |
Number of Residues | 4 |
Details | binding site for residue PEG C 509 |
Chain | Residue |
C | ALA334 |
C | THR335 |
C | ILE337 |
C | HOH711 |
site_id | AG6 |
Number of Residues | 5 |
Details | binding site for residue PEG C 510 |
Chain | Residue |
C | HIS40 |
C | PHE196 |
C | EDO506 |
C | PGE511 |
C | HOH608 |
site_id | AG7 |
Number of Residues | 9 |
Details | binding site for residue PGE C 511 |
Chain | Residue |
C | LEU187 |
C | PHE196 |
C | LEU197 |
C | PHE236 |
C | GLY237 |
C | EDO504 |
C | EDO506 |
C | PEG510 |
C | HOH656 |
site_id | AG8 |
Number of Residues | 10 |
Details | binding site for residue PG4 C 512 |
Chain | Residue |
B | SER210 |
C | TYR42 |
C | LYS234 |
C | GLY237 |
C | LEU238 |
C | THR332 |
C | SER336 |
C | EDO508 |
C | HOH639 |
C | HOH674 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 3 |
Details | ACT_SITE: ACT_SITE => ECO:0000269|PubMed:29056341 |
Chain | Residue | Details |
A | ASP320 | |
B | ASP320 | |
C | ASP320 |
site_id | SWS_FT_FI2 |
Number of Residues | 15 |
Details | BINDING: BINDING => ECO:0000269|PubMed:29056341, ECO:0007744|PDB:5VXC, ECO:0007744|PDB:5VXO |
Chain | Residue | Details |
A | TYR50 | |
B | ILE272 | |
C | TYR50 | |
C | LYS57 | |
C | LYS61 | |
C | ARG107 | |
C | ILE272 | |
A | LYS57 | |
A | LYS61 | |
A | ARG107 | |
A | ILE272 | |
B | TYR50 | |
B | LYS57 | |
B | LYS61 | |
B | ARG107 |
site_id | SWS_FT_FI3 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:29056341, ECO:0007744|PDB:5VXC |
Chain | Residue | Details |
A | GLU171 | |
A | ASP206 | |
B | GLU171 | |
B | ASP206 | |
C | GLU171 | |
C | ASP206 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8R4N0 |
Chain | Residue | Details |
A | LYS57 | |
A | LYS61 | |
B | LYS57 | |
B | LYS61 | |
C | LYS57 | |
C | LYS61 |
site_id | SWS_FT_FI5 |
Number of Residues | 6 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q8R4N0 |
Chain | Residue | Details |
A | LYS82 | |
A | LYS92 | |
B | LYS82 | |
B | LYS92 | |
C | LYS82 | |
C | LYS92 |
site_id | SWS_FT_FI6 |
Number of Residues | 3 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q8R4N0 |
Chain | Residue | Details |
A | LYS309 | |
B | LYS309 | |
C | LYS309 |