MolNFT v1 · #108618 · protein + RNA
The crystal structure of the large ribosomal subunit of staphylococcus aureus
4WCE · 23S rRNA: “The crystal structure of the large ribosomal subunit of staphylococcus aureus”. X-ray diffraction, 3 ligands (SPD, MN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #108618 on GenesisL1: 3D structure, binding sites…
- PDB
- 4WCE
- Type
- protein + RNA
- Length
- 5,819 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, Q2YYP6, 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, 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 | 2708 | — | — |
| Y | 5S rRNA | rna | 114 | — | — |
| A | 50S ribosomal protein L2 | protein | 269 | 3% helix, 13% strand | P60430 |
| B | 50S ribosomal protein L3 | protein | 215 | 9% helix, 34% strand | Q2YYP6 |
| C | 50S ribosomal protein L4 | protein | 199 | 28% helix, 11% strand | Q2FW07 |
| D | 50S ribosomal protein L5 | protein | 166 | 26% helix, 9% strand | Q2FW18 |
| E | 50S ribosomal protein L6 | protein | 156 | 20% helix, 6% strand | Q2FW21 |
| G | 50S ribosomal protein L13 | protein | 145 | 32% helix, 12% strand | Q2FW38 |
| H | 50S ribosomal protein L14 | protein | 122 | 8% helix, 34% strand | Q2FW16 |
| I | 50S ribosomal protein L15 | protein | 131 | 8% helix, 5% strand | P0A0F8 |
| J | 50S ribosomal protein L16 | protein | 141 | 18% helix, 23% strand | Q2FW13 |
| K | 50S ribosomal protein L17 | protein | 119 | 49% helix, 17% strand | Q2FW33 |
| L | 50S ribosomal protein L18 | protein | 110 | 27% helix, 5% strand | Q2FW22 |
| M | 50S ribosomal protein L19 | protein | 110 | 9% helix, 35% strand | Q2FZ42 |
| N | 50S ribosomal protein L20 | protein | 116 | 73% helix, 0% strand | Q2FXQ1 |
| O | 50S ribosomal protein L21 | protein | 102 | 0% helix, 37% strand | Q2FXS8 |
| P | 50S ribosomal protein L22 | protein | 112 | 38% helix, 38% strand | Q2FW11 |
| Q | 50S ribosomal protein L23 | protein | 89 | 21% helix, 25% strand | Q2FW08 |
| R | 50S ribosomal protein L24 | protein | 100 | 3% helix, 20% strand | Q2FW17 |
| S | 50S ribosomal protein L25 | protein | 167 | 9% helix, 32% strand | Q2FJE0 |
| T | 50S ribosomal protein L27 | protein | 75 | 0% helix, 39% strand | Q2FXT0 |
| U | 50S ribosomal protein L28 | protein | 46 | 0% helix, 30% strand | Q2FZ60 |
| V | 50S ribosomal protein L29 | protein | 65 | 66% helix, 0% strand | Q2FW14 |
| W | 50S ribosomal protein L30 | protein | 58 | 36% helix, 24% strand | P0A0G2 |
| Z | 50S ribosomal protein L32 | protein | 43 | 23% helix, 14% strand | Q2FZF1 |
| 2 | 50S ribosomal protein L34 | protein | 44 | 61% helix, 0% strand | Q2FUQ0 |
| 3 | 50S ribosomal protein L35 | protein | 60 | 22% helix, 10% strand | Q2FXQ0 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 8% helix, 30% strand | Q2FW29 |
Ligands and binding sites
- SPD · Spermidine · ligand · 4 copies · chains X, C, G
- MN · Manganese (II) ion · metal · 231 copies · chains X, A, 2, G, J, M, Q, T, B, C, K, I, 4, Y, R
- MG · Magnesium ion · metal · 91 copies · chains X, N, Y, C, B, G, O, I
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains X, C, U, N, I, Z
- EOH · Ethanol · additive · 7 copies · chains X, R
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains X, G
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 | 982 | 0.88 | 0.91 | 99 | MN, MG |
| 2 | 1079 | 0.88 | 0.90 | 104 | MPD, MN, MG |
| 3 | 604 | 0.87 | 0.93 | 80 | MPD, MG, MN |
| 4 | 990 | 0.87 | 0.89 | 94 | MN, MG, EPE |
| 5 | 1010 | 0.86 | 0.88 | 89 | MN |
Interfaces
53 interfaces between chains.
- X–A · 5918 Ų buried · 122 hydrogen bonds · protein-nucleic
- X–B · 5046 Ų buried · 126 hydrogen bonds · protein-nucleic
- X–C · 3965 Ų buried · 70 hydrogen bonds · protein-nucleic
- X–N · 3956 Ų buried · 108 hydrogen bonds · protein-nucleic
- X–I · 3658 Ų buried · 64 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
- 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
- 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 0.97
- 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
- Q2YYP6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (Q2YYP6) · a predicted model of the same protein · chain B 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
- 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
- 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 0.95
- 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 0.95
- Q2FW14 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L29 (Q2FW14) · a predicted model of the same protein · chain V 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
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 Q2YYP6
- 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 4WCE · PDBe 4WCE · UniProt P60430 · UniProt Q2YYP6 · 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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