Research workbench
The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with linezolid
Analyse The crystal structure of the large ribosomal subunit of staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WFA
- Type
- protein + RNA
- Length
- 5,801 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
- UniProt
- P60430, Q2FW06, Q2FW07, Q2FW18, Q2FW21, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2FJE0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FZF1, Q2FUQ0, Q2FXQ0, Q2FW29
- Ligands
- SPD, ZLD, MG, MN, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 28 distinct chains · 20% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 23S rRNA | rna | 2711 | — | — |
| Y | 5S rRNA | rna | 114 | — | — |
| A | 50S ribosomal protein L2 | protein | 268 | 3% helix, 10% strand | P60430 |
| B | 50S ribosomal protein L3 | protein | 215 | 9% helix, 32% strand | Q2FW06 |
| C | 50S ribosomal protein L4 | protein | 199 | 25% helix, 9% strand | Q2FW07 |
| D | 50S ribosomal protein L5 | protein | 155 | 26% helix, 7% strand | Q2FW18 |
| E | 50S ribosomal protein L6 | protein | 157 | 20% helix, 16% strand | Q2FW21 |
| G | 50S ribosomal protein L13 | protein | 145 | 28% helix, 13% strand | Q2FW38 |
| H | 50S ribosomal protein L14 | protein | 122 | 7% helix, 39% strand | Q2FW16 |
| I | 50S ribosomal protein L15 | protein | 131 | 5% helix, 7% strand | P0A0F8 |
| J | 50S ribosomal protein L16 | protein | 138 | 19% helix, 23% strand | Q2FW13 |
| K | 50S ribosomal protein L17 | protein | 119 | 49% helix, 15% strand | Q2FW33 |
| L | 50S ribosomal protein L18 | protein | 108 | 20% helix, 4% strand | Q2FW22 |
| M | 50S ribosomal protein L19 | protein | 109 | 8% helix, 31% strand | Q2FZ42 |
| N | 50S ribosomal protein L20 | protein | 116 | 73% helix, 0% strand | Q2FXQ1 |
| O | 50S ribosomal protein L21 | protein | 101 | 0% helix, 45% strand | Q2FXS8 |
| P | 50S ribosomal protein L22 | protein | 112 | 38% helix, 33% strand | Q2FW11 |
| Q | 50S ribosomal protein L23 | protein | 88 | 26% helix, 26% strand | Q2FW08 |
| R | 50S ribosomal protein L24 | protein | 100 | 3% helix, 21% strand | Q2FW17 |
| S | 50S ribosomal protein L25 | protein | 167 | 9% helix, 34% strand | Q2FJE0 |
| T | 50S ribosomal protein L27 | protein | 75 | 0% helix, 37% strand | Q2FXT0 |
| U | 50S ribosomal protein L28 | protein | 44 | 0% helix, 9% strand | Q2FZ60 |
| V | 50S ribosomal protein L29 | protein | 65 | 68% helix, 0% strand | Q2FW14 |
| W | 50S ribosomal protein L30 | protein | 57 | 37% helix, 25% strand | P0A0G2 |
| Z | 50S ribosomal protein L32 | protein | 44 | 23% helix, 9% strand | Q2FZF1 |
| 2 | 50S ribosomal protein L34 | protein | 44 | 52% helix, 0% strand | Q2FUQ0 |
| 3 | 50S ribosomal protein L35 | protein | 60 | 5% helix, 10% strand | Q2FXQ0 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 8% helix, 32% strand | Q2FW29 |
Ligands and binding sites
- SPD · Spermidine · ligand · 9 copies · chains X, C, J, S
- ZLD · N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide · ligand · chains X
- MG · Magnesium ion · metal · 246 copies · chains X, Q, I, A, K, Y, B, N, J, T, 2, G, 4, S, C, O, W, Z
- MN · Manganese (II) ion · metal · 195 copies · chains X, I, B, G, K, W, J, A, M, C, U, Y, Z
- NA · Sodium ion · metal · chains X
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains X
- EOH · Ethanol · additive · 5 copies · chains X, Y
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains X, B, T, N
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 | 1001 | 0.88 | 0.90 | 98 | MG, MN |
| 2 | 921 | 0.87 | 0.90 | 109 | MPD, MG, MN |
| 3 | 1031 | 0.87 | 0.89 | 90 | MN, MG, EPE |
| 4 | 1047 | 0.86 | 0.88 | 99 | MG, MN, EPE |
| 5 | 830 | 0.86 | 0.89 | 69 | MN, MG |
Interfaces
52 interfaces between chains.
- X–A · 5692 Ų buried · 113 hydrogen bonds · protein-nucleic
- X–B · 4954 Ų buried · 115 hydrogen bonds · protein-nucleic
- X–C · 4076 Ų buried · 79 hydrogen bonds · protein-nucleic
- X–N · 3918 Ų buried · 118 hydrogen bonds · protein-nucleic
- X–I · 3456 Ų buried · 72 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q2FXQ1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (Q2FXQ1) · a predicted model of the same protein · chain N against A, TM-score 0.98
- Q2FW16 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (Q2FW16) · a predicted model of the same protein · chain H against A, TM-score 0.98
- Q2FW07 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (Q2FW07) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P60430 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60430) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q2FW38 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (Q2FW38) · a predicted model of the same protein · chain G against A, TM-score 0.97
- Q2FW11 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (Q2FW11) · a predicted model of the same protein · chain P against A, TM-score 0.96
- Q2FW33 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (Q2FW33) · a predicted model of the same protein · chain K against A, TM-score 0.96
- Q2FXS8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (Q2FXS8) · a predicted model of the same protein · chain O against A, TM-score 0.96
- Q2FW06 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (Q2FW06) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P0A0G2 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L30 (P0A0G2) · a predicted model of the same protein · chain W against A, TM-score 0.95
- Q2FJE0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L25 (Q2FJE0) · a predicted model of the same protein · chain S against A, TM-score 0.94
- Q2FW18 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L5 (Q2FW18) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P60430
- Every structure of UniProt Q2FW06
- Every structure of UniProt Q2FW07
- Every structure of UniProt Q2FW18
- Every structure of UniProt Q2FW21
- Every structure of UniProt Q2FW38
- Every structure of UniProt Q2FW16
- Every structure of UniProt P0A0F8
- Every structure of UniProt Q2FW13
- Every structure of UniProt Q2FW33
- Every structure of UniProt Q2FW22
- Every structure of UniProt Q2FZ42
- Every structure of UniProt Q2FXQ1
- Every structure of UniProt Q2FXS8
- Every structure of UniProt Q2FW11
- Every structure of UniProt Q2FW08
- Every structure of UniProt Q2FW17
- Every structure of UniProt Q2FJE0
- Every structure of UniProt Q2FXT0
- Every structure of UniProt Q2FZ60
- Every structure of UniProt Q2FW14
- Every structure of UniProt P0A0G2
- Every structure of UniProt Q2FZF1
- Every structure of UniProt Q2FUQ0
- Every structure of UniProt Q2FXQ0
- Every structure of UniProt Q2FW29
- Elsewhere: RCSB PDB 4WFA · PDBe 4WFA · UniProt P60430 · UniProt Q2FW06 · UniProt Q2FW07 · UniProt Q2FW18 · UniProt Q2FW21 · UniProt Q2FW38 · UniProt Q2FW16 · UniProt P0A0F8 · UniProt Q2FW13 · UniProt Q2FW33 · UniProt Q2FW22 · UniProt Q2FZ42 · UniProt Q2FXQ1 · UniProt Q2FXS8 · UniProt Q2FW11 · UniProt Q2FW08 · UniProt Q2FW17 · UniProt Q2FJE0 · UniProt Q2FXT0 · UniProt Q2FZ60 · UniProt Q2FW14 · UniProt P0A0G2 · UniProt Q2FZF1 · UniProt Q2FUQ0 · UniProt Q2FXQ0 · UniProt Q2FW29
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