MolNFT v1 · #190716 · protein
Re-refinement of damage free X-ray structure of bovine cytochrome C oxidase at 1.9 ångström resolution
7Y44: “Re-refinement of damage free X-ray structure of bovine cytochrome C oxidase at 1.9 ångström resolution”. X-ray diffraction, 14 ligands (CHD, PGV, TGL). MolNFT v1 #190716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Y44
- Type
- protein
- Length
- 3,558 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- CHD, PGV, TGL, PEK, HEA, CDL, CUA, PSC, NA, CU, MG, ZN, PER, PO4
Structure
x-ray diffraction · 13 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | — | protein | 514 | — | P00396 |
| B, O | — | protein | 227 | — | P68530 |
| C, P | — | protein | 259 | — | P00415 |
| D, Q | — | protein | 144 | — | P00423 |
| E, R | — | protein | 105 | — | P00426 |
| F, S | — | protein | 98 | — | P00428 |
| G, T | — | protein | 84 | — | P07471 |
| H, U | — | protein | 79 | — | P00429 |
| I, V | — | protein | 73 | — | P04038 |
| J, W | — | protein | 58 | — | P07470 |
| K, X | — | protein | 49 | — | P13183 |
| L, Y | — | protein | 46 | — | P00430 |
| M, Z | — | protein | 43 | — | P10175 |
Ligands and binding sites
- CHD · Cholic acid · ligand · 11 copies · chains C, J, A, P, G, N, O, L, M, W, B, T, X, Y, Z
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 8 copies · chains A, C, D, K, M, H, P, T, N, Q, X, Z, G, U
- TGL · Tristearoylglycerol · ligand · 6 copies · chains A, B, I, D, 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 A, C, G, F, N, O, T, P, 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
- NA · Sodium ion · metal · 4 copies · chains A, C, N, P
- CU · Copper (II) ion · metal · 2 copies · chains A, N
- MG · Magnesium ion · metal · 2 copies · chains A, B, N, O
- ZN · Zinc ion · metal · 2 copies · chains F, S
- PER · Peroxide ion · ion · 2 copies · chains A, N
- PO4 · Phosphate ion · ion · 2 copies · chains H, U
- EDO · 1,2-ethanediol · additive · 49 copies · chains A, M, F, B, C, H, G, J, L, N, Z, Q, S, O, P, U, Y, W, T, R
- DMU · Decyl-beta-D-maltopyranoside · additive · 23 copies · chains B, C, J, D, G, K, A, L, M, O, V, P, W, Q, X, T, N, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7Y44 · Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9… · 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 7Y44 · PDBe 7Y44 · 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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