MolNFT v1 · #191316 · protein
Mammalian civ with gdn bound
8D4T · Cytochrome C oxidase subunit 1: “Mammalian civ with gdn bound”. Electron microscopy, 8 ligands (HEA, PGV, PEK), 20 pockets (best druggability 0.91). MolNFT v1 #191316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8D4T
- Type
- protein
- Length
- 1,738 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 7.1.1.9
- UniProt
- P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430
- Ligands
- HEA, PGV, PEK, 9Z9, CU, MG, NA, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 13 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 512 | 70% helix, 1% strand | P00396 |
| O | Cytochrome C oxidase subunit 2 | protein | 227 | 35% helix, 25% strand | P68530 |
| P | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 258 | 76% helix, 0% strand | P00415 |
| Q | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 137 | 53% helix, 4% strand | P00423 |
| R | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 102 | 69% helix, 1% strand | P00426 |
| S | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 91 | 16% helix, 29% strand | P00428 |
| T | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 72 | 35% helix, 3% strand | P07471 |
| U | Cytochrome C oxidase subunit 6B1 | protein | 78 | 59% helix, 1% strand | P00429 |
| V | Cytochrome C oxidase subunit 6C | protein | 70 | 73% helix, 1% strand | P04038 |
| W | Cytochrome C oxidase subunit 7A1, mitochondrial | protein | 55 | 69% helix, 0% strand | P07470 |
| X | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 47 | 57% helix, 0% strand | P13183 |
| Y | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 46 | 63% helix, 0% strand | P00430 |
| M | Cytochrome C oxidase subunit 8A, mitochondrial | protein | 43 | 67% helix, 2% strand | — |
Ligands and binding sites
- HEA · Heme-A · ligand · 2 copies · chains N, O
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 2 copies · chains N, P, S
- PEK · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5E,8E,11E,14E)-icosa-5,8, 11,14-tetraenoate · ligand · chains N, P, T
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains N, P
- CU · Copper (II) ion · metal · 3 copies · chains N, O
- MG · Magnesium ion · metal · chains N, O
- NA · Sodium ion · metal · chains N
- ZN · Zinc ion · metal · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.91 | 0.92 | 125 | HEA |
| 2 | 829 | 0.86 | 0.88 | 83 | PGV |
| 3 | 1029 | 0.83 | 0.84 | 102 | empty |
| 4 | 73 | 0.75 | 0.98 | 36 | empty |
| 5 | 887 | 0.74 | 0.78 | 71 | empty |
Interfaces
34 interfaces between chains.
- N–O · 3549 Ų buried · 35 hydrogen bonds · protein-protein
- N–P · 2614 Ų buried · 20 hydrogen bonds · protein-protein
- N–Y · 1813 Ų buried · 19 hydrogen bonds · protein-protein
- P–T · 1671 Ų buried · 19 hydrogen bonds · protein-protein
- O–V · 1646 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified, 1 covalent (disulfide, formylation, covalent ligand).
Compared structures
- 8D4T · Mammalian CIV with GDN bound · the same entry in another collection · chain X against X, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00396
- Every structure of UniProt P68530
- Every structure of UniProt P00415
- Every structure of UniProt P00423
- Every structure of UniProt P00426
- Every structure of UniProt P00428
- Every structure of UniProt P07471
- Every structure of UniProt P00429
- Every structure of UniProt P04038
- Every structure of UniProt P07470
- Every structure of UniProt P13183
- Every structure of UniProt P00430
- Elsewhere: RCSB PDB 8D4T · PDBe 8D4T · UniProt P00396 · UniProt P68530 · UniProt P00415 · UniProt P00423 · UniProt P00426 · UniProt P00428 · UniProt P07471 · UniProt P00429 · UniProt P04038 · UniProt P07470 · UniProt P13183 · UniProt P00430
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