4COO
Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001958 | biological_process | endochondral ossification |
| A | 0001974 | biological_process | blood vessel remodeling |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004122 | molecular_function | cystathionine beta-synthase activity |
| A | 0004124 | molecular_function | cysteine synthase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006534 | biological_process | cysteine metabolic process |
| A | 0006535 | biological_process | cysteine biosynthetic process from serine |
| A | 0006563 | biological_process | L-serine metabolic process |
| A | 0006565 | biological_process | L-serine catabolic process |
| A | 0006801 | biological_process | superoxide metabolic process |
| A | 0008152 | biological_process | metabolic process |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0010749 | biological_process | regulation of nitric oxide mediated signal transduction |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019343 | biological_process | cysteine biosynthetic process via cystathionine |
| A | 0019344 | biological_process | cysteine biosynthetic process |
| A | 0019346 | biological_process | transsulfuration |
| A | 0019448 | biological_process | L-cysteine catabolic process |
| A | 0019825 | molecular_function | oxygen binding |
| A | 0019899 | molecular_function | enzyme binding |
| A | 0020037 | molecular_function | heme binding |
| A | 0021587 | biological_process | cerebellum morphogenesis |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0031625 | molecular_function | ubiquitin protein ligase binding |
| A | 0031667 | biological_process | response to nutrient levels |
| A | 0042262 | biological_process | DNA protection |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0043066 | biological_process | negative regulation of apoptotic process |
| A | 0043418 | biological_process | homocysteine catabolic process |
| A | 0044272 | biological_process | sulfur compound biosynthetic process |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050421 | molecular_function | nitrite reductase (NO-forming) activity |
| A | 0050667 | biological_process | homocysteine metabolic process |
| A | 0051593 | biological_process | response to folic acid |
| A | 0060135 | biological_process | maternal process involved in female pregnancy |
| A | 0060351 | biological_process | cartilage development involved in endochondral bone morphogenesis |
| A | 0070025 | molecular_function | carbon monoxide binding |
| A | 0070026 | molecular_function | nitric oxide binding |
| A | 0070814 | biological_process | hydrogen sulfide biosynthetic process |
| A | 0071456 | biological_process | cellular response to hypoxia |
| A | 0072341 | molecular_function | modified amino acid binding |
| A | 0080146 | molecular_function | L-cysteine desulfhydrase activity |
| A | 0097746 | biological_process | blood vessel diameter maintenance |
| A | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
| B | 0001958 | biological_process | endochondral ossification |
| B | 0001974 | biological_process | blood vessel remodeling |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004122 | molecular_function | cystathionine beta-synthase activity |
| B | 0004124 | molecular_function | cysteine synthase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006534 | biological_process | cysteine metabolic process |
| B | 0006535 | biological_process | cysteine biosynthetic process from serine |
| B | 0006563 | biological_process | L-serine metabolic process |
| B | 0006565 | biological_process | L-serine catabolic process |
| B | 0006801 | biological_process | superoxide metabolic process |
| B | 0008152 | biological_process | metabolic process |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| B | 0010749 | biological_process | regulation of nitric oxide mediated signal transduction |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019343 | biological_process | cysteine biosynthetic process via cystathionine |
| B | 0019344 | biological_process | cysteine biosynthetic process |
| B | 0019346 | biological_process | transsulfuration |
| B | 0019448 | biological_process | L-cysteine catabolic process |
| B | 0019825 | molecular_function | oxygen binding |
| B | 0019899 | molecular_function | enzyme binding |
| B | 0020037 | molecular_function | heme binding |
| B | 0021587 | biological_process | cerebellum morphogenesis |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0031625 | molecular_function | ubiquitin protein ligase binding |
| B | 0031667 | biological_process | response to nutrient levels |
| B | 0042262 | biological_process | DNA protection |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0043066 | biological_process | negative regulation of apoptotic process |
| B | 0043418 | biological_process | homocysteine catabolic process |
| B | 0044272 | biological_process | sulfur compound biosynthetic process |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050421 | molecular_function | nitrite reductase (NO-forming) activity |
| B | 0050667 | biological_process | homocysteine metabolic process |
| B | 0051593 | biological_process | response to folic acid |
| B | 0060135 | biological_process | maternal process involved in female pregnancy |
| B | 0060351 | biological_process | cartilage development involved in endochondral bone morphogenesis |
| B | 0070025 | molecular_function | carbon monoxide binding |
| B | 0070026 | molecular_function | nitric oxide binding |
| B | 0070814 | biological_process | hydrogen sulfide biosynthetic process |
| B | 0071456 | biological_process | cellular response to hypoxia |
| B | 0072341 | molecular_function | modified amino acid binding |
| B | 0080146 | molecular_function | L-cysteine desulfhydrase activity |
| B | 0097746 | biological_process | blood vessel diameter maintenance |
| B | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE HEM A 1549 |
| Chain | Residue |
| A | SER50 |
| A | ARG224 |
| A | ALA226 |
| A | LEU230 |
| A | TYR233 |
| A | ARG266 |
| A | EDO1552 |
| A | HOH2091 |
| A | HOH2096 |
| A | ARG51 |
| A | CYS52 |
| A | THR53 |
| A | TRP54 |
| A | GLU62 |
| A | SER63 |
| A | PRO64 |
| A | HIS65 |
| site_id | AC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE HEM B 1539 |
| Chain | Residue |
| B | SER50 |
| B | ARG51 |
| B | CYS52 |
| B | THR53 |
| B | PRO59 |
| B | GLU62 |
| B | SER63 |
| B | PRO64 |
| B | HIS65 |
| B | ALA226 |
| B | PRO229 |
| B | TYR233 |
| B | ARG266 |
| B | EDO1544 |
| B | HOH2102 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE ACT A 1550 |
| Chain | Residue |
| A | LYS119 |
| A | THR146 |
| A | SER147 |
| A | ASN149 |
| A | THR150 |
| A | GLN222 |
| A | HOH2047 |
| A | HOH2048 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE ACT B 1540 |
| Chain | Residue |
| B | LYS119 |
| B | THR146 |
| B | SER147 |
| B | ASN149 |
| B | THR150 |
| B | GLN222 |
| B | HOH2018 |
| B | HOH2019 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE ACT B 1541 |
| Chain | Residue |
| A | EDO1559 |
| B | GLU187 |
| B | VAL189 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ACT B 1542 |
| Chain | Residue |
| A | EDO1554 |
| A | HOH2190 |
| B | TRP409 |
| B | LEU530 |
| site_id | AC7 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE PLP A 1551 |
| Chain | Residue |
| A | LYS119 |
| A | ASN149 |
| A | SER254 |
| A | VAL255 |
| A | GLY256 |
| A | THR257 |
| A | GLY258 |
| A | GLY259 |
| A | THR260 |
| A | GLY305 |
| A | ILE306 |
| A | SER349 |
| A | PRO375 |
| A | ASP376 |
| A | HOH2047 |
| A | HOH2094 |
| A | HOH2106 |
| A | HOH2107 |
| site_id | AC8 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE PLP B 1543 |
| Chain | Residue |
| B | LYS119 |
| B | ASN149 |
| B | SER254 |
| B | VAL255 |
| B | GLY256 |
| B | THR257 |
| B | GLY258 |
| B | GLY259 |
| B | THR260 |
| B | GLU304 |
| B | GLY305 |
| B | ILE306 |
| B | SER349 |
| B | PRO375 |
| B | ASP376 |
| B | HOH2019 |
| B | HOH2044 |
| B | HOH2047 |
| B | HOH2048 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 1552 |
| Chain | Residue |
| A | SER50 |
| A | PRO229 |
| A | THR262 |
| A | ARG266 |
| A | THR313 |
| A | VAL314 |
| A | HEM1549 |
| site_id | BC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 1553 |
| Chain | Residue |
| A | ALA195 |
| A | PHE197 |
| A | SER202 |
| A | HIS203 |
| A | TYR308 |
| A | ASP309 |
| A | HOH2081 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 1544 |
| Chain | Residue |
| B | SER50 |
| B | THR262 |
| B | ARG266 |
| B | THR313 |
| B | VAL314 |
| B | HEM1539 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 1554 |
| Chain | Residue |
| A | GLU187 |
| A | HOH2190 |
| B | ACT1542 |
| B | ACT1546 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 1555 |
| Chain | Residue |
| A | LYS485 |
| A | GLN486 |
| A | PHE487 |
| A | HOH2174 |
| A | HOH2191 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1556 |
| Chain | Residue |
| A | LEU315 |
| A | ASP316 |
| A | ARG317 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PE4 A 1557 |
| Chain | Residue |
| A | ASP198 |
| A | PRO200 |
| A | GLU436 |
| A | ARG439 |
| B | GLY462 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 1558 |
| Chain | Residue |
| A | LYS172 |
| A | MET173 |
| A | GLY305 |
| A | ILE306 |
| A | HOH2125 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 1545 |
| Chain | Residue |
| B | LYS172 |
| B | MET173 |
| B | GLY305 |
| B | ILE306 |
| B | HOH2058 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ACT B 1546 |
| Chain | Residue |
| A | ILE188 |
| A | VAL189 |
| A | EDO1554 |
| B | SER500 |
| B | GLU504 |
| B | LEU529 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 1559 |
| Chain | Residue |
| A | LEU539 |
| A | LEU540 |
| A | HOH2189 |
| B | ACT1541 |
Functional Information from PROSITE/UniProt
| site_id | PS00901 |
| Number of Residues | 19 |
| Details | CYS_SYNTHASE Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. KcEffn.AGgSVKdRiSlrM |
| Chain | Residue | Details |
| A | LYS108-MET126 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: axial binding residue => ECO:0000269|PubMed:11483494, ECO:0000269|PubMed:12173932 |
| Chain | Residue | Details |
| A | CYS52 | |
| A | HIS65 | |
| B | CYS52 | |
| B | HIS65 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11483494, ECO:0000269|PubMed:12173932 |
| Chain | Residue | Details |
| B | GLY256 | |
| B | SER349 | |
| A | ASN149 | |
| A | GLY256 | |
| A | SER349 | |
| B | ASN149 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER27 | |
| B | SER27 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:11483494, ECO:0000269|PubMed:12173932 |
| Chain | Residue | Details |
| A | LYS119 | |
| B | LYS119 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER199 | |
| A | SER199 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000269|PubMed:17087506 |
| Chain | Residue | Details |
| A | LYS211 | |
| B | LYS211 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 1 |
| Details | M-CSA 713 |
| Chain | Residue | Details |
| A | LYS119 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay |
| site_id | MCSA2 |
| Number of Residues | 1 |
| Details | M-CSA 713 |
| Chain | Residue | Details |
| B | LYS119 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay |
