5XDO
Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001662 | biological_process | behavioral fear response |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005741 | cellular_component | mitochondrial outer membrane |
| A | 0005757 | cellular_component | mitochondrial permeability transition pore complex |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006090 | biological_process | pyruvate metabolic process |
| A | 0006811 | biological_process | monoatomic ion transport |
| A | 0006820 | biological_process | monoatomic anion transport |
| A | 0006869 | biological_process | lipid transport |
| A | 0006915 | biological_process | apoptotic process |
| A | 0007268 | biological_process | chemical synaptic transmission |
| A | 0007270 | biological_process | neuron-neuron synaptic transmission |
| A | 0007612 | biological_process | learning |
| A | 0008142 | molecular_function | oxysterol binding |
| A | 0008289 | molecular_function | lipid binding |
| A | 0008308 | molecular_function | voltage-gated monoatomic anion channel activity |
| A | 0015288 | molecular_function | porin activity |
| A | 0015485 | molecular_function | cholesterol binding |
| A | 0016020 | cellular_component | membrane |
| A | 0019901 | molecular_function | protein kinase binding |
| A | 0030855 | biological_process | epithelial cell differentiation |
| A | 0031210 | molecular_function | phosphatidylcholine binding |
| A | 0031966 | cellular_component | mitochondrial membrane |
| A | 0036444 | biological_process | calcium import into the mitochondrion |
| A | 0042645 | cellular_component | mitochondrial nucleoid |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0043065 | biological_process | positive regulation of apoptotic process |
| A | 0043066 | biological_process | negative regulation of apoptotic process |
| A | 0044325 | molecular_function | transmembrane transporter binding |
| A | 0045121 | cellular_component | membrane raft |
| A | 0045202 | cellular_component | synapse |
| A | 0046930 | cellular_component | pore complex |
| A | 0055085 | biological_process | transmembrane transport |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0097001 | molecular_function | ceramide binding |
| A | 0098656 | biological_process | monoatomic anion transmembrane transport |
| A | 0110099 | biological_process | negative regulation of calcium import into the mitochondrion |
| A | 1901524 | biological_process | regulation of mitophagy |
| A | 1903146 | biological_process | regulation of autophagy of mitochondrion |
| A | 1905091 | biological_process | positive regulation of type 2 mitophagy |
| A | 1990542 | biological_process | mitochondrial transmembrane transport |
| A | 2000378 | biological_process | negative regulation of reactive oxygen species metabolic process |
| B | 0001662 | biological_process | behavioral fear response |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005741 | cellular_component | mitochondrial outer membrane |
| B | 0005757 | cellular_component | mitochondrial permeability transition pore complex |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006090 | biological_process | pyruvate metabolic process |
| B | 0006811 | biological_process | monoatomic ion transport |
| B | 0006820 | biological_process | monoatomic anion transport |
| B | 0006869 | biological_process | lipid transport |
| B | 0006915 | biological_process | apoptotic process |
| B | 0007268 | biological_process | chemical synaptic transmission |
| B | 0007270 | biological_process | neuron-neuron synaptic transmission |
| B | 0007612 | biological_process | learning |
| B | 0008142 | molecular_function | oxysterol binding |
| B | 0008289 | molecular_function | lipid binding |
| B | 0008308 | molecular_function | voltage-gated monoatomic anion channel activity |
| B | 0015288 | molecular_function | porin activity |
| B | 0015485 | molecular_function | cholesterol binding |
| B | 0016020 | cellular_component | membrane |
| B | 0019901 | molecular_function | protein kinase binding |
| B | 0030855 | biological_process | epithelial cell differentiation |
| B | 0031210 | molecular_function | phosphatidylcholine binding |
| B | 0031966 | cellular_component | mitochondrial membrane |
| B | 0036444 | biological_process | calcium import into the mitochondrion |
| B | 0042645 | cellular_component | mitochondrial nucleoid |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0043065 | biological_process | positive regulation of apoptotic process |
| B | 0043066 | biological_process | negative regulation of apoptotic process |
| B | 0044325 | molecular_function | transmembrane transporter binding |
| B | 0045121 | cellular_component | membrane raft |
| B | 0045202 | cellular_component | synapse |
| B | 0046930 | cellular_component | pore complex |
| B | 0055085 | biological_process | transmembrane transport |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0097001 | molecular_function | ceramide binding |
| B | 0098656 | biological_process | monoatomic anion transmembrane transport |
| B | 0110099 | biological_process | negative regulation of calcium import into the mitochondrion |
| B | 1901524 | biological_process | regulation of mitophagy |
| B | 1903146 | biological_process | regulation of autophagy of mitochondrion |
| B | 1905091 | biological_process | positive regulation of type 2 mitophagy |
| B | 1990542 | biological_process | mitochondrial transmembrane transport |
| B | 2000378 | biological_process | negative regulation of reactive oxygen species metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue SPD A 301 |
| Chain | Residue |
| A | TYR7 |
| A | LEU10 |
| A | GLN154 |
| A | ASN183 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue OCT A 302 |
| Chain | Residue |
| A | ASN214 |
| B | PHE219 |
| B | OCT302 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue OCT A 303 |
| Chain | Residue |
| A | SER167 |
| A | PHE169 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | binding site for residue LNK A 304 |
| Chain | Residue |
| A | TYR153 |
| site_id | AC5 |
| Number of Residues | 1 |
| Details | binding site for residue HEX A 306 |
| Chain | Residue |
| A | ARG120 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue SPD B 301 |
| Chain | Residue |
| B | TYR7 |
| B | LEU10 |
| B | ARG15 |
| B | HIS181 |
| B | THR182 |
| B | ASN183 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue OCT B 302 |
| Chain | Residue |
| A | LEU208 |
| A | OCT302 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue OCT B 303 |
| Chain | Residue |
| B | PHE190 |
| B | TRP210 |
| B | GLY213 |
Functional Information from PROSITE/UniProt
| site_id | PS00558 |
| Number of Residues | 23 |
| Details | EUKARYOTIC_PORIN Eukaryotic mitochondrial porin signature. YqiDPdAcfsAKVNNssliGLgY |
| Chain | Residue | Details |
| A | TYR225-TYR247 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 328 |
| Details | TRANSMEM: Beta stranded => ECO:0000269|PubMed:18755977, ECO:0000269|PubMed:18832158 |
| Chain | Residue | Details |
| A | LEU26-SER35 | |
| A | LEU150-GLU158 | |
| A | ARG163-THR175 | |
| A | PHE178-ASN185 | |
| A | GLU189-VAL198 | |
| A | LEU202-THR211 | |
| A | ARG218-ILE227 | |
| A | ALA231-ASN238 | |
| A | LEU242-LEU251 | |
| A | GLY254-LEU263 | |
| A | HIS273-GLN282 | |
| A | LEU39-ALA47 | |
| B | LEU26-SER35 | |
| B | LEU39-ALA47 | |
| B | VAL54-TRP64 | |
| B | LEU69-ASN76 | |
| B | THR80-ASP89 | |
| B | LEU95-SER104 | |
| B | ASN111-ARG120 | |
| B | ILE123-ASP130 | |
| B | SER137-GLY145 | |
| B | LEU150-GLU158 | |
| A | VAL54-TRP64 | |
| B | ARG163-THR175 | |
| B | PHE178-ASN185 | |
| B | GLU189-VAL198 | |
| B | LEU202-THR211 | |
| B | ARG218-ILE227 | |
| B | ALA231-ASN238 | |
| B | LEU242-LEU251 | |
| B | GLY254-LEU263 | |
| B | HIS273-GLN282 | |
| A | LEU69-ASN76 | |
| A | THR80-ASP89 | |
| A | LEU95-SER104 | |
| A | ASN111-ARG120 | |
| A | ILE123-ASP130 | |
| A | SER137-GLY145 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q60932 |
| Chain | Residue | Details |
| A | LYS12 | |
| A | LYS20 | |
| B | LYS12 | |
| B | LYS20 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18755977 |
| Chain | Residue | Details |
| A | LEU242 | |
| A | SER260 | |
| B | LEU242 | |
| B | SER260 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | SITE: Involved in ceramide and phosphatidylcholine binding. Critical for channel structural stability and gating => ECO:0000269|PubMed:31015432, ECO:0000305|PubMed:18832158 |
| Chain | Residue | Details |
| A | GLU73 | |
| B | GLU73 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylalanine => ECO:0000269|PubMed:2559745, ECO:0000269|Ref.12, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:22223895, ECO:0007744|PubMed:22814378, ECO:0007744|PubMed:25944712 |
| Chain | Residue | Details |
| A | ALA2 | |
| B | ALA2 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q9Z2L0 |
| Chain | Residue | Details |
| A | SER13 | |
| B | SER13 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q60932 |
| Chain | Residue | Details |
| A | THR19 | |
| B | THR19 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q60932 |
| Chain | Residue | Details |
| A | LYS20 | |
| B | LYS20 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q60932 |
| Chain | Residue | Details |
| A | TYR67 | |
| B | TYR67 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | THR107 | |
| B | THR107 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:Q60932 |
| Chain | Residue | Details |
| A | LYS109 | |
| B | LYS109 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by NEK1 => ECO:0000269|PubMed:20230784 |
| Chain | Residue | Details |
| A | SER193 | |
| B | SER193 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER240 | |
| B | SER240 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q60932 |
| Chain | Residue | Details |
| A | LYS252 | |
| B | LYS252 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS266 | |
| B | LYS266 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:32047033 |
| Chain | Residue | Details |
| A | LYS12 | |
| B | LYS12 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25621951, ECO:0000269|PubMed:32047033 |
| Chain | Residue | Details |
| A | LYS53 | |
| A | LYS110 | |
| A | LYS274 | |
| B | LYS53 | |
| B | LYS110 | |
| B | LYS274 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:32047033 |
| Chain | Residue | Details |
| A | LYS20 | |
| B | LYS20 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25621951 |
| Chain | Residue | Details |
| A | LYS61 | |
| A | LYS161 | |
| B | LYS61 | |
| B | LYS161 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:25621951, ECO:0000269|PubMed:32047033 |
| Chain | Residue | Details |
| A | LYS109 | |
| B | LYS109 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:25621951 |
| Chain | Residue | Details |
| A | LYS266 | |
| B | LYS266 |
