Research workbench
The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with bc-3205
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
- 4WFB
- Type
- protein + RNA
- Length
- 5,771 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, 3LK, MN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 28 distinct chains · 21% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 23S rRNA | rna | 2707 | — | — |
| Y | 5S rRNA | rna | 114 | — | — |
| A | 50S ribosomal protein L2 | protein | 271 | 4% helix, 13% strand | P60430 |
| B | 50S ribosomal protein L3 | protein | 215 | 9% helix, 31% strand | Q2FW06 |
| C | 50S ribosomal protein L4 | protein | 199 | 29% helix, 10% strand | Q2FW07 |
| D | 50S ribosomal protein L5 | protein | 139 | 31% helix, 8% strand | Q2FW18 |
| E | 50S ribosomal protein L6 | protein | 156 | 22% helix, 8% strand | Q2FW21 |
| G | 50S ribosomal protein L13 | protein | 145 | 24% helix, 15% strand | Q2FW38 |
| H | 50S ribosomal protein L14 | protein | 122 | 8% helix, 34% strand | Q2FW16 |
| I | 50S ribosomal protein L15 | protein | 131 | 5% helix, 8% strand | P0A0F8 |
| J | 50S ribosomal protein L16 | protein | 136 | 21% helix, 23% strand | Q2FW13 |
| K | 50S ribosomal protein L17 | protein | 119 | 46% helix, 15% strand | Q2FW33 |
| L | 50S ribosomal protein L18 | protein | 110 | 31% helix, 6% strand | Q2FW22 |
| M | 50S ribosomal protein L19 | protein | 109 | 8% helix, 32% strand | Q2FZ42 |
| N | 50S ribosomal protein L20 | protein | 116 | 73% helix, 0% strand | Q2FXQ1 |
| O | 50S ribosomal protein L21 | protein | 101 | 0% helix, 50% strand | Q2FXS8 |
| P | 50S ribosomal protein L22 | protein | 109 | 40% helix, 34% strand | Q2FW11 |
| Q | 50S ribosomal protein L23 | protein | 89 | 18% helix, 29% strand | Q2FW08 |
| R | 50S ribosomal protein L24 | protein | 100 | 0% helix, 24% strand | Q2FW17 |
| S | 50S ribosomal protein L25 | protein | 157 | 11% helix, 32% strand | Q2FJE0 |
| T | 50S ribosomal protein L27 | protein | 75 | 0% helix, 37% strand | Q2FXT0 |
| U | 50S ribosomal protein L28 | protein | 44 | 9% helix, 14% strand | Q2FZ60 |
| V | 50S ribosomal protein L29 | protein | 65 | 72% helix, 0% strand | Q2FW14 |
| W | 50S ribosomal protein L30 | protein | 57 | 33% helix, 16% strand | P0A0G2 |
| Z | 50S ribosomal protein L32 | protein | 44 | 23% helix, 9% strand | Q2FZF1 |
| 2 | 50S ribosomal protein L34 | protein | 44 | 61% helix, 0% strand | Q2FUQ0 |
| 3 | 50S ribosomal protein L35 | protein | 60 | 27% helix, 10% strand | Q2FXQ0 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 8% helix, 32% strand | Q2FW29 |
Ligands and binding sites
- SPD · Spermidine · ligand · 11 copies · chains X, G, I, C
- 3LK · Bc-3205 · ligand · chains X
- MN · Manganese (II) ion · metal · 311 copies · chains X, N, I, B, G, A, Q, K, C, 4, M, Y, R
- MG · Magnesium ion · metal · 111 copies · chains X, B, G, A, C, P, I, 3, H, Y, E, N, O
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 15 copies · chains X, Z, G, T, N
- EOH · Ethanol · additive · 13 copies · chains X, C, Y, K, W
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains X, B, J
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 | 946 | 0.88 | 0.91 | 102 | MG, MN |
| 2 | 601 | 0.87 | 0.93 | 71 | MN, MG |
| 3 | 981 | 0.86 | 0.88 | 101 | MPD, MG, MN |
| 4 | 697 | 0.86 | 0.90 | 71 | MN, MG |
| 5 | 798 | 0.85 | 0.89 | 76 | MN, SPD |
Interfaces
53 interfaces between chains.
- X–A · 5535 Ų buried · 94 hydrogen bonds · protein-nucleic
- X–B · 4900 Ų buried · 117 hydrogen bonds · protein-nucleic
- X–C · 3961 Ų buried · 67 hydrogen bonds · protein-nucleic
- X–N · 3921 Ų buried · 112 hydrogen bonds · protein-nucleic
- X–I · 3377 Ų buried · 66 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 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
- 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
- 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
- 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 0.97
- 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
- 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 0.97
- Q2FW22 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L18 (Q2FW22) · a predicted model of the same protein · chain L 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
- 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 0.96
- 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
- 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 0.95
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 4WFB · PDBe 4WFB · 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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