MolNFT v1 · #136916 · protein + RNA
Cryo-EM structure of the large ribosomal subunit from mycobacterium tuberculosis bound with a potent linezolid analog
5V7Q · 50S ribosomal protein L32: “Cryo-EM structure of the large ribosomal subunit from mycobacterium tuberculosis bound with a potent…”. Electron microscopy, 1 ligand (917), 20 pockets (best druggability 0.88). MolNFT v1 #136916 on…
- PDB
- 5V7Q
- Type
- protein + RNA
- Length
- 6,449 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L32; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S…
- UniProt
- A0A045IMI5, A0A045HU86, A0A1L6JUG3, A0A045KKY9, A0A1L6JSF4, A0A045HLX7, A0A045H5T7, A0A045HU18, A0A045J9H1, A0A045HUU0, A0A045JJU1, A0A045JW48, A0A0T9D5H2, A0A0U0S3A8, A0A0T7M0A0, A0A045IWV9, A0A045IVA2, A0A045JK28, A0A045IDD2, A0A045KJ85, A0A1N6MHB1, A0A045H760, A0A045J9M3, A0A045IXU4, A0A045JAK4, A0A045K0G1, A0A045IDB8, A0A045IQ64, A0A045H4J2
- Ligands
- 917
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 31 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 50S ribosomal protein L32 | protein | 53 | 34% helix, 4% strand | A0A045IMI5 |
| 1 | 50S ribosomal protein L33 | protein | 48 | 0% helix, 44% strand | A0A045HU86 |
| 2 | 50S ribosomal protein L34 | protein | 42 | 60% helix, 0% strand | A0A1L6JUG3 |
| 3 | 50S ribosomal protein L35 | protein | 62 | 31% helix, 16% strand | A0A045KKY9 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 0% helix, 38% strand | A0A1L6JSF4 |
| 6 | 50S ribosomal protein L31 | protein | 45 | 7% helix, 20% strand | A0A045HLX7 |
| A | 23S rRNA | rna | 3118 | — | — |
| B | 5S ribosomal RNA | rna | 115 | — | — |
| C | 50S ribosomal protein L2 | protein | 272 | 6% helix, 25% strand | A0A045H5T7 |
| D | 50S ribosomal protein L3 | protein | 213 | 10% helix, 36% strand | A0A045HU18 |
| E | 50S ribosomal protein L4 | protein | 207 | 31% helix, 8% strand | A0A045J9H1 |
| F | 50S ribosomal protein L5 | protein | 170 | 29% helix, 20% strand | A0A045HUU0 |
| G | 50S ribosomal protein L6 | protein | 174 | 20% helix, 26% strand | A0A045JJU1 |
| H | 50S ribosomal protein L9 | protein | 47 | 9% helix, 17% strand | A0A045JW48 |
| J | 50S ribosomal protein L13 | protein | 146 | 32% helix, 19% strand | A0A0T9D5H2 |
| K | 50S ribosomal protein L14 | protein | 121 | 3% helix, 40% strand | A0A0U0S3A8 |
| L | 50S ribosomal protein L15 | protein | 142 | 24% helix, 8% strand | A0A0T7M0A0 |
| M | 50S ribosomal protein L16 | protein | 134 | 21% helix, 13% strand | A0A045IWV9 |
| N | 50S ribosomal protein L17 | protein | 116 | 53% helix, 15% strand | A0A045IVA2 |
| O | 50S ribosomal protein L18 | protein | 116 | 39% helix, 19% strand | A0A045JK28 |
| P | 50S ribosomal protein L19 | protein | 112 | 12% helix, 38% strand | A0A045IDD2 |
| Q | 50S ribosomal protein L20 | protein | 122 | 74% helix, 0% strand | A0A045KJ85 |
| R | Lsu ribosomal protein L21P | protein | 98 | 4% helix, 52% strand | A0A1N6MHB1 |
| S | 50S ribosomal protein L22 | protein | 113 | 36% helix, 35% strand | A0A045H760 |
| T | 50S ribosomal protein L23 | protein | 98 | 20% helix, 28% strand | A0A045J9M3 |
| U | 50S ribosomal protein L24 | protein | 90 | 3% helix, 31% strand | A0A045IXU4 |
| V | 50S ribosomal protein L25 | protein | 177 | 7% helix, 34% strand | A0A045JAK4 |
| W | 50S ribosomal protein L27 | protein | 74 | 0% helix, 23% strand | A0A045K0G1 |
| X | 50S ribosomal protein L28 | protein | 63 | 8% helix, 25% strand | A0A045IDB8 |
| Y | 50S ribosomal protein L29 | protein | 65 | 74% helix, 0% strand | A0A045IQ64 |
| Z | 50S ribosomal protein L30 | protein | 59 | 27% helix, 22% strand | A0A045H4J2 |
Ligands and binding sites
- 917 · N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide · ligand · chains A
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 | 984 | 0.88 | 0.90 | 96 | empty |
| 2 | 500 | 0.85 | 0.93 | 54 | empty |
| 3 | 1100 | 0.85 | 0.87 | 75 | empty |
| 4 | 828 | 0.85 | 0.88 | 61 | empty |
| 5 | 607 | 0.85 | 0.91 | 61 | empty |
Interfaces
58 interfaces between chains.
- A–C · 7610 Ų buried · 153 hydrogen bonds · protein-nucleic
- A–D · 5018 Ų buried · 86 hydrogen bonds · protein-nucleic
- A–L · 4667 Ų buried · 101 hydrogen bonds · protein-nucleic
- A–E · 4511 Ų buried · 68 hydrogen bonds · protein-nucleic
- A–Q · 4458 Ų buried · 95 hydrogen bonds · protein-nucleic
Compared structures
- 5V7Q · Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound… · the same entry in another collection · chain Z against Z, 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 A0A045IMI5
- Every structure of UniProt A0A045HU86
- Every structure of UniProt A0A1L6JUG3
- Every structure of UniProt A0A045KKY9
- Every structure of UniProt A0A1L6JSF4
- Every structure of UniProt A0A045HLX7
- Every structure of UniProt A0A045H5T7
- Every structure of UniProt A0A045HU18
- Every structure of UniProt A0A045J9H1
- Every structure of UniProt A0A045HUU0
- Every structure of UniProt A0A045JJU1
- Every structure of UniProt A0A045JW48
- Every structure of UniProt A0A0T9D5H2
- Every structure of UniProt A0A0U0S3A8
- Every structure of UniProt A0A0T7M0A0
- Every structure of UniProt A0A045IWV9
- Every structure of UniProt A0A045IVA2
- Every structure of UniProt A0A045JK28
- Every structure of UniProt A0A045IDD2
- Every structure of UniProt A0A045KJ85
- Every structure of UniProt A0A1N6MHB1
- Every structure of UniProt A0A045H760
- Every structure of UniProt A0A045J9M3
- Every structure of UniProt A0A045IXU4
- Every structure of UniProt A0A045JAK4
- Every structure of UniProt A0A045K0G1
- Every structure of UniProt A0A045IDB8
- Every structure of UniProt A0A045IQ64
- Every structure of UniProt A0A045H4J2
- Elsewhere: RCSB PDB 5V7Q · PDBe 5V7Q · UniProt A0A045IMI5 · UniProt A0A045HU86 · UniProt A0A1L6JUG3 · UniProt A0A045KKY9 · UniProt A0A1L6JSF4 · UniProt A0A045HLX7 · UniProt A0A045H5T7 · UniProt A0A045HU18 · UniProt A0A045J9H1 · UniProt A0A045HUU0 · UniProt A0A045JJU1 · UniProt A0A045JW48 · UniProt A0A0T9D5H2 · UniProt A0A0U0S3A8 · UniProt A0A0T7M0A0 · UniProt A0A045IWV9 · UniProt A0A045IVA2 · UniProt A0A045JK28 · UniProt A0A045IDD2 · UniProt A0A045KJ85 · UniProt A0A1N6MHB1 · UniProt A0A045H760 · UniProt A0A045J9M3 · UniProt A0A045IXU4 · UniProt A0A045JAK4 · UniProt A0A045K0G1 · UniProt A0A045IDB8 · UniProt A0A045IQ64 · UniProt A0A045H4J2
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