MolNFT v1 · #158124 · protein
Time-resolved sfx structure of the pr intermediate of cytochrome C oxidase at room temperature
6NKN · Cytochrome C oxidase subunit 1: “Time-resolved sfx structure of the pr intermediate of cytochrome C oxidase at room temperature”. X-ray diffraction, 14 ligands (PGV, CHD, TGL), 20 pockets (best druggability 0.91). MolNFT v1 #158124…
- PDB
- 6NKN
- Type
- protein
- Length
- 3,546 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 1.9.3.1
- UniProt
- P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- PGV, CHD, TGL, PEK, HEA, CDL, CUA, PSC, CU, MG, NA, ZN, O, OH
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 16 distinct chains · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 514 | 71% helix, 2% strand | P00396 |
| B, O | Cytochrome C oxidase subunit 2 | protein | 227 | 32% helix, 26% strand | P68530 |
| C, P | Cytochrome C oxidase subunit 3 | protein | 259 | 76% helix, 0% strand | P00415 |
| D | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 52% helix, 3% strand | P00423 |
| E, R | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 105 | 65% helix, 1% strand | P00426 |
| F | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 96 | 16% helix, 27% strand | P00428 |
| G, T | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 84 | 27% helix, 2% strand | P07471 |
| H | Cytochrome C oxidase subunit 6B1 | protein | 78 | 59% helix, 1% strand | P00429 |
| I, V | Cytochrome C oxidase subunit 6C | protein | 73 | 70% helix, 1% strand | P04038 |
| J, W | Cytochrome C oxidase subunit 7A1, mitochondrial | protein | 58 | 67% helix, 0% strand | P07470 |
| K, X | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 49 | 53% helix, 0% strand | P13183 |
| L, Y | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 46 | 59% helix, 0% strand | P00430 |
| M, Z | Cytochrome C oxidase subunit 8B, mitochondrial | protein | 43 | 67% helix, 5% strand | P10175 |
| Q | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 139 | 50% helix, 4% strand | P00423 |
| S | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 94 | 17% helix, 23% strand | P00428 |
| U | Cytochrome C oxidase subunit 6B1 | protein | 79 | 57% helix, 1% strand | P00429 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 8 copies · chains A, D, K, M, C, H, P, T, F, N, Q, X, Z, S, G, U
- CHD · Cholic acid · ligand · 8 copies · chains A, B, T, C, P, G, N, O, J, W
- TGL · Tristearoylglycerol · ligand · 6 copies · chains A, B, D, I, L, N, O, V, Q, Y
- PEK · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5E,8E,11E,14E)-icosa-5,8, 11,14-tetraenoate · ligand · 6 copies · chains C, G, N, O, A, P, T, B
- HEA · Heme-A · ligand · 4 copies · chains A, B, N, O
- CDL · Cardiolipin · ligand · 4 copies · chains C, J, G, N, O, P, W, A, B, T
- CUA · Dinuclear copper ion · ligand · 2 copies · chains B, O
- PSC · (7R,17E,20E)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosa-17,20-dien-1-aminium 4-oxide · ligand · 2 copies · chains A, B, E, I, N, O, R, V
- CU · Copper (II) ion · metal · 2 copies · chains A, N
- MG · Magnesium ion · metal · 2 copies · chains A, B, N, O
- NA · Sodium ion · metal · 2 copies · chains A, N
- ZN · Zinc ion · metal · 2 copies · chains F, S
- O · Oxygen atom · ion · 2 copies · chains A, N
- OH · Hydroxide ion · ion · 2 copies · chains A, N
- DMU · Decyl-beta-D-maltopyranoside · additive · 4 copies · chains C, G, A, D, M, N, Q, Y, Z, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.91 | 0.93 | 119 | HEA, O, OH |
| 2 | 1176 | 0.91 | 0.92 | 124 | HEA, O, OH |
| 3 | 820 | 0.86 | 0.88 | 78 | PGV |
| 4 | 1173 | 0.85 | 0.85 | 106 | PGV, PEK |
| 5 | 1024 | 0.84 | 0.85 | 100 | empty |
Interfaces
78 interfaces between chains.
- N–O · 3580 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3558 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2619 Ų buried · 17 hydrogen bonds · protein-protein
- N–P · 2610 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 1824 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (disulfide, formylation, acetylation, phosphorylation).
Compared structures
- 6NKN · Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room… · the same entry in another collection · chain K against K, 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
- Every structure of UniProt P10175
- Elsewhere: RCSB PDB 6NKN · PDBe 6NKN · UniProt P00396 · UniProt P68530 · UniProt P00415 · UniProt P00423 · UniProt P00426 · UniProt P00428 · UniProt P07471 · UniProt P00429 · UniProt P04038 · UniProt P07470 · UniProt P13183 · UniProt P00430 · UniProt P10175
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