MolNFT v1 · #64540 · protein + RNA
Co-crystal structure of homoharringtonine bound to the large ribosomal subunit
3G6E · 23S ribosomal RNA: “Co-crystal structure of homoharringtonine bound to the large ribosomal subunit”. X-ray diffraction, 7 ligands (HMT, SR, MG), 20 pockets (best druggability 0.90). MolNFT v1 #64540 on GenesisL1: 3D structure…
- PDB
- 3G6E
- Type
- protein + RNA
- Length
- 6,651 residues
- Chains
- 31
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L2P; 50S ribosomal protein L3P; 50S ribosomal…
- UniProt
- P20276, P20279, P12735, P14124, P14135, P12743, P15825, P60617, P14122, P29198, P22450, P12737, P60618, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P60619, P32410, P22452, P32411
- Ligands
- HMT, SR, MG, NA, CD, K, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 31 distinct chains · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2754 | — | — |
| A | 50S ribosomal protein L2P | protein | 237 | 11% helix, 25% strand | P20276 |
| B | 50S ribosomal protein L3P | protein | 337 | 14% helix, 33% strand | P20279 |
| C | 50S ribosomal protein L4P | protein | 246 | 31% helix, 14% strand | P12735 |
| D | 50S ribosomal protein L5P | protein | 140 | 24% helix, 23% strand | P14124 |
| E | 50S ribosomal protein L6P | protein | 172 | 22% helix, 41% strand | P14135 |
| F | 50S ribosomal protein L7AE | protein | 119 | 43% helix, 16% strand | P12743 |
| G | 50S ribosomal protein L10E | protein | 29 | 79% helix, 0% strand | P15825 |
| H | 50S ribosomal protein L10E | protein | 160 | 24% helix, 29% strand | P60617 |
| I | 50S ribosomal protein L11P | protein | 70 | 31% helix, 9% strand | P14122 |
| J | 50S ribosomal protein L13P | protein | 142 | 39% helix, 16% strand | P29198 |
| K | 50S ribosomal protein L14P | protein | 132 | 8% helix, 38% strand | P22450 |
| L | 50S ribosomal protein L15P | protein | 145 | 17% helix, 15% strand | P12737 |
| M | 50S ribosomal protein L15E | protein | 194 | 33% helix, 16% strand | P60618 |
| N | 50S ribosomal protein L18P | protein | 186 | 38% helix, 13% strand | P14123 |
| O | 50S ribosomal protein L18E | protein | 115 | 43% helix, 19% strand | P12733 |
| P | 50S ribosomal protein L19E | protein | 143 | 57% helix, 4% strand | P14119 |
| Q | 50S ribosomal protein L21E | protein | 95 | 14% helix, 32% strand | P12734 |
| R | 50S ribosomal protein L22P | protein | 150 | 31% helix, 31% strand | P10970 |
| S | 50S ribosomal protein L23P | protein | 81 | 33% helix, 31% strand | P12732 |
| T | 50S ribosomal protein L24P | protein | 119 | 29% helix, 29% strand | P10972 |
| U | 50S ribosomal protein L24E | protein | 53 | 21% helix, 19% strand | P14116 |
| V | 50S ribosomal protein L29P | protein | 65 | 74% helix, 0% strand | P10971 |
| W | 50S ribosomal protein L30P | protein | 154 | 38% helix, 14% strand | P14121 |
| X | 50S ribosomal protein L31E | protein | 82 | 40% helix, 29% strand | P18138 |
| Y | 50S ribosomal protein L32E | protein | 142 | 20% helix, 12% strand | P12736 |
| Z | 50S ribosomal protein L37AE | protein | 73 | 26% helix, 15% strand | P60619 |
| 1 | 50S ribosomal protein L37E | protein | 56 | 16% helix, 11% strand | P32410 |
| 2 | 50S ribosomal protein L39E | protein | 46 | 41% helix, 0% strand | P22452 |
| 3 | 50S ribosomal protein L44E | protein | 92 | 13% helix, 33% strand | P32411 |
| 9 | 5S ribosomal RNA | rna | 122 | — | — |
Ligands and binding sites
- HMT · (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine · ligand · chains 0
- SR · Strontium ion · metal · 108 copies · chains 0, B, H, M, T, 1, L, 2, 3, 9, Y, A, F, J, R, S
- MG · Magnesium ion · metal · 93 copies · chains 0, A, C, R, S, B, W, Y, 3, P, M, K, T, 2, 9
- NA · Sodium ion · metal · 75 copies · chains 0, B, 2, H, Y, R, T, J, C, M, 3, L, Q, S, D, 9
- CD · Cadmium ion · metal · 5 copies · chains O, U, Z, 1, 3
- K · Potassium ion · metal · 2 copies · chains 0, M
- CL · Chloride ion · ion · 22 copies · chains 0, 2, Q, K, L, J, Y, W, A, B, E, M, D, N, O, R, 3
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 | 1035 | 0.90 | 0.92 | 101 | MG, NA, SR |
| 2 | 882 | 0.88 | 0.91 | 109 | MG, CL, SR |
| 3 | 973 | 0.87 | 0.89 | 88 | empty |
| 4 | 926 | 0.86 | 0.89 | 72 | SR |
| 5 | 1168 | 0.86 | 0.88 | 105 | MG, SR, NA |
Interfaces
55 interfaces between chains.
- 0–B · 7459 Ų buried · 230 hydrogen bonds · protein-nucleic
- 0–M · 6577 Ų buried · 179 hydrogen bonds · protein-nucleic
- 0–A · 6386 Ų buried · 183 hydrogen bonds · protein-nucleic
- 0–C · 5661 Ų buried · 149 hydrogen bonds · protein-nucleic
- 0–P · 4422 Ų buried · 135 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 3G6E · Co-crystal structure of Homoharringtonine bound to the large ribosomal subunit · the same entry in another collection · chain J against J, 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 P20276
- Every structure of UniProt P20279
- Every structure of UniProt P12735
- Every structure of UniProt P14124
- Every structure of UniProt P14135
- Every structure of UniProt P12743
- Every structure of UniProt P15825
- Every structure of UniProt P60617
- Every structure of UniProt P14122
- Every structure of UniProt P29198
- Every structure of UniProt P22450
- Every structure of UniProt P12737
- Every structure of UniProt P60618
- Every structure of UniProt P14123
- Every structure of UniProt P12733
- Every structure of UniProt P14119
- Every structure of UniProt P12734
- Every structure of UniProt P10970
- Every structure of UniProt P12732
- Every structure of UniProt P10972
- Every structure of UniProt P14116
- Every structure of UniProt P10971
- Every structure of UniProt P14121
- Every structure of UniProt P18138
- Every structure of UniProt P12736
- Every structure of UniProt P60619
- Every structure of UniProt P32410
- Every structure of UniProt P22452
- Every structure of UniProt P32411
- Elsewhere: RCSB PDB 3G6E · PDBe 3G6E · UniProt P20276 · UniProt P20279 · UniProt P12735 · UniProt P14124 · UniProt P14135 · UniProt P12743 · UniProt P15825 · UniProt P60617 · UniProt P14122 · UniProt P29198 · UniProt P22450 · UniProt P12737 · UniProt P60618 · UniProt P14123 · UniProt P12733 · UniProt P14119 · UniProt P12734 · UniProt P10970 · UniProt P12732 · UniProt P10972 · UniProt P14116 · UniProt P10971 · UniProt P14121 · UniProt P18138 · UniProt P12736 · UniProt P60619 · UniProt P32410 · UniProt P22452 · UniProt P32411
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