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The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui
Analyse The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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