5XDN
Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 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 | 3 |
Details | binding site for residue D12 A 301 |
Chain | Residue |
A | TYR146 |
B | ASN238 |
B | SER241 |
site_id | AC2 |
Number of Residues | 2 |
Details | binding site for residue HEX A 302 |
Chain | Residue |
A | MET129 |
B | D10301 |
site_id | AC3 |
Number of Residues | 3 |
Details | binding site for residue OCT A 303 |
Chain | Residue |
A | ILE138 |
A | PHE157 |
B | PHE178 |
site_id | AC4 |
Number of Residues | 2 |
Details | binding site for residue D10 B 301 |
Chain | Residue |
B | TYR173 |
A | HEX302 |
site_id | AC5 |
Number of Residues | 2 |
Details | binding site for residue D10 B 302 |
Chain | Residue |
A | PHE190 |
B | TYR118 |
site_id | AC6 |
Number of Residues | 3 |
Details | binding site for residue D12 B 303 |
Chain | Residue |
A | ARG93 |
A | TYR118 |
B | TRP210 |
site_id | AC7 |
Number of Residues | 3 |
Details | binding site for residue HEX B 304 |
Chain | Residue |
B | GLU73 |
B | LEU81 |
B | THR83 |
site_id | AC8 |
Number of Residues | 1 |
Details | binding site for residue HEX B 305 |
Chain | Residue |
B | PHE169 |
site_id | AC9 |
Number of Residues | 1 |
Details | binding site for residue HEX B 306 |
Chain | Residue |
B | THR204 |
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 |