MolNFT v1 · #60627 · protein + RNA
The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui
3CXC · 23S ribosomal RNA: “The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui”. X-ray diffraction, 6 ligands (SLD, MG, NA), 20 pockets (best druggability 0.89). MolNFT v1 #60627 on…
- PDB
- 3CXC
- Type
- protein + RNA
- Length
- 6,580 residues
- Chains
- 31
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 5S ribosomal RNA; 5'-R(*CP*CP*A)-3'; Ribosomal protein L2; Ribosomal…
- UniProt
- P20276, P20279, P12735, P14124, P14135, P12743, P15825, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P32410, P22452, P32411
- Ligands
- SLD, MG, NA, CD, K, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 31 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2754 | — | — |
| 9 | 5S ribosomal RNA | rna | 122 | — | — |
| 4 | 5'-R(*CP*CP*A)-3' | rna | 3 | — | — |
| A | Ribosomal protein L2 | protein | 237 | 14% helix, 24% strand | P20276 |
| B | Ribosomal protein L3 | protein | 337 | 14% helix, 32% strand | P20279 |
| C | Ribosomal protein L4 | protein | 246 | 35% helix, 14% strand | P12735 |
| D | Ribosomal protein L5 | protein | 140 | 27% helix, 19% strand | P14124 |
| E | Ribosomal protein L6 | protein | 172 | 22% helix, 42% strand | P14135 |
| F | Ribosomal protein L7AE | protein | 119 | 49% helix, 15% strand | P12743 |
| G | Ribosomal protein L10 | protein | 29 | 79% helix, 0% strand | P15825 |
| H | Ribosomal protein L10E | protein | 156 | 13% helix, 28% strand | — |
| I | Ribosomal protein L13 | protein | 142 | 40% helix, 15% strand | P29198 |
| J | Ribosomal protein L14 | protein | 132 | 6% helix, 36% strand | P22450 |
| K | Ribosomal protein L15 | protein | 145 | 19% helix, 16% strand | P12737 |
| L | Ribosomal protein L15E | protein | 194 | 31% helix, 13% strand | — |
| M | Ribosomal protein L18 | protein | 186 | 38% helix, 13% strand | P14123 |
| N | Ribosomal protein L18E | protein | 115 | 44% helix, 23% strand | P12733 |
| O | Ribosomal protein L19E | protein | 143 | 60% helix, 4% strand | P14119 |
| P | Ribosomal protein L21E | protein | 95 | 15% helix, 32% strand | P12734 |
| Q | Ribosomal protein L22 | protein | 150 | 33% helix, 31% strand | P10970 |
| R | Ribosomal protein L23 | protein | 81 | 33% helix, 31% strand | P12732 |
| S | Ribosomal protein L24 | protein | 119 | 29% helix, 29% strand | P10972 |
| T | Ribosomal protein L24E | protein | 53 | 21% helix, 19% strand | P14116 |
| U | Ribosomal protein L29 | protein | 65 | 75% helix, 0% strand | P10971 |
| V | Ribosomal protein L30 | protein | 154 | 40% helix, 14% strand | P14121 |
| W | Ribosomal protein L31E | protein | 82 | 37% helix, 28% strand | P18138 |
| X | Ribosomal protein L32E | protein | 142 | 28% helix, 12% strand | P12736 |
| Y | Ribosomal protein L37AE | protein | 73 | 36% helix, 22% strand | — |
| Z | Ribosomal protein L37E | protein | 56 | 13% helix, 16% strand | P32410 |
| 1 | Ribosomal protein L39E | protein | 46 | 41% helix, 0% strand | P22452 |
| 2 | Ribosomal protein L44E | protein | 92 | 14% helix, 30% strand | P32411 |
Ligands and binding sites
- SLD · (3Z)-N-[(4E)-5-(4-{(5S)-5-[(acetylamino)methyl]-2-oxo-1,3-oxazolidin-3-yl}-2-fluorophenyl)pent-4-en-1-yl]-3-(4-methyl-2,6-dioxo-1,6-dihydropyrimidin-5(2H)-ylidene)propanamide · ligand · chains 0, 4
- MG · Magnesium ion · metal · 117 copies · chains 0, A, B, C, R, Q, V, E, 1, Z, X, 2, O, L, 9, 4, Y, J, S
- NA · Sodium ion · metal · 86 copies · chains 0, K, B, 1, X, Q, S, 9, I, C, L, 2, D, A, H, P, R
- CD · Cadmium ion · metal · 5 copies · chains N, T, Y, Z, 2
- K · Potassium ion · metal · 2 copies · chains 0, L
- CL · Chloride ion · ion · 22 copies · chains 0, 1, K, I, X, A, B, E, J, L, D, M, N, P, Q, 2
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 | 943 | 0.89 | 0.91 | 112 | MG, CL |
| 2 | 968 | 0.87 | 0.90 | 97 | MG, NA |
| 3 | 1183 | 0.87 | 0.88 | 114 | empty |
| 4 | 1014 | 0.86 | 0.88 | 92 | CL |
| 5 | 1010 | 0.86 | 0.88 | 101 | empty |
Interfaces
54 interfaces between chains.
- 0–B · 7368 Ų buried · 225 hydrogen bonds · protein-nucleic
- 0–L · 6902 Ų buried · 187 hydrogen bonds · protein-nucleic
- 0–A · 6231 Ų buried · 175 hydrogen bonds · protein-nucleic
- 0–C · 5593 Ų buried · 138 hydrogen bonds · protein-nucleic
- 0–O · 4370 Ų buried · 128 hydrogen bonds · protein-nucleic
Compared structures
- 3CXC · The structure of an enhanced oxazolidi inhibitor bound to the 50S ribosomal subunit of H.… · the same entry in another collection · chain 0 against 0, 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 P29198
- Every structure of UniProt P22450
- Every structure of UniProt P12737
- 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 P32410
- Every structure of UniProt P22452
- Every structure of UniProt P32411
- Elsewhere: RCSB PDB 3CXC · PDBe 3CXC · UniProt P20276 · UniProt P20279 · UniProt P12735 · UniProt P14124 · UniProt P14135 · UniProt P12743 · UniProt P15825 · UniProt P29198 · UniProt P22450 · UniProt P12737 · 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 P32410 · UniProt P22452 · UniProt P32411
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