Research workbench
The structure of the transition state analogue "dan" bound to the large ribosomal subunit of haloarcula marismortui
Analyse The structure of the transition state analogue "dan" bound to the large… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VQM
- Type
- protein + RNA
- Length
- 6,656 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 5S ribosomal RNA; 5'-R(*CP*CP*(PPU)P*(PO2)P*(DA)P*C*C)-3'); 50S…
- UniProt
- P20276, P12735, P14124, P14135, P12743, P15825, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P32410, P22452, P32411
- Ligands
- PPU, PO2, SR, MG, NA, CD, K, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 32 distinct chains · 30% helix, 22% 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*(PPU)P*(PO2)P*(DA)P*C*C)-3') | rna | 5 | — | — |
| A | 50S ribosomal protein L2P | protein | 237 | 13% helix, 25% strand | P20276 |
| B | 50S ribosomal protein L3P | protein | 337 | 14% helix, 32% strand | — |
| C | 50S ribosomal protein L4E | protein | 246 | 33% helix, 14% strand | P12735 |
| D | 50S ribosomal protein L5P | protein | 140 | 23% helix, 23% strand | P14124 |
| E | 50S ribosomal protein L6P | protein | 172 | 22% helix, 41% strand | P14135 |
| F | 50S ribosomal protein L7AE | protein | 119 | 47% helix, 13% strand | P12743 |
| G | Acidic ribosomal protein P0 homolog | protein | 29 | 79% helix, 0% strand | P15825 |
| H | 50S ribosomal protein L10E | protein | 160 | 24% helix, 28% strand | — |
| J | 50S ribosomal protein L13P | protein | 142 | 41% helix, 15% strand | P29198 |
| K | 50S ribosomal protein L14P | protein | 132 | 8% helix, 41% strand | P22450 |
| L | 50S ribosomal protein L15P | protein | 145 | 20% helix, 16% strand | P12737 |
| M | 50S ribosomal protein L15E | protein | 194 | 35% helix, 16% strand | — |
| N | 50S ribosomal protein L18P | protein | 186 | 39% helix, 13% strand | P14123 |
| O | 50S ribosomal protein L18E | protein | 115 | 46% helix, 23% strand | P12733 |
| P | 50S ribosomal protein L19E | protein | 143 | 64% helix, 4% strand | P14119 |
| Q | 50S ribosomal protein L21E | protein | 95 | 14% helix, 32% strand | P12734 |
| R | 50S ribosomal protein L22P | protein | 150 | 33% helix, 31% strand | P10970 |
| S | 50S ribosomal protein L23P | protein | 81 | 32% helix, 31% strand | P12732 |
| T | 50S ribosomal protein L24P | protein | 119 | 29% helix, 29% strand | P10972 |
| U | 50S ribosomal protein L24E | protein | 53 | 21% helix, 19% strand | P14116 |
| V | 50S ribosomal protein L29P | protein | 65 | 77% helix, 0% strand | P10971 |
| W | 50S ribosomal protein L30P | protein | 154 | 37% helix, 15% strand | P14121 |
| X | 50S ribosomal protein L31E | protein | 82 | 43% helix, 30% strand | P18138 |
| Y | 50S ribosomal protein L32E | protein | 142 | 24% helix, 13% strand | P12736 |
| Z | 50S ribosomal protein L37AE | protein | 73 | 34% helix, 19% strand | — |
| 1 | 50S ribosomal protein L37E | protein | 56 | 13% helix, 16% strand | P32410 |
| 2 | 50S ribosomal protein L39E | protein | 46 | 41% helix, 0% strand | P22452 |
| 3 | 50S ribosomal protein L44E | protein | 92 | 14% helix, 33% strand | P32411 |
| I | 50S ribosomal protein L11P | protein | 70 | 39% helix, 9% strand | — |
Ligands and binding sites
- PPU · Puromycin-5'-monophosphate · ligand · chains 0, 4
- PO2 · Hypophosphite · ligand · chains 0, 4
- SR · Strontium ion · metal · 114 copies · chains 0, B, H, M, T, 4, L, 3, 1, 9, C, Y, J, A, F, R, S
- MG · Magnesium ion · metal · 94 copies · chains 0, A, C, 1, S, M, R, 9, B, W, Y, P, 3, 4, K, T, 2
- NA · Sodium ion · metal · 75 copies · chains 0, B, 2, Y, T, J, C, M, L, 9, D, H, Q, R, S, 3
- CD · Cadmium ion · metal · 5 copies · chains O, U, Z, 1, 3
- K · Potassium ion · metal · 2 copies · chains 0, M
- CL · Chloride ion · ion · 22 copies · chains 0, 2, Q, K, L, J, Y, A, B, E, M, D, N, O, R, 3
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 | 1048 | 0.90 | 0.92 | 101 | MG, NA, SR |
| 2 | 1197 | 0.87 | 0.88 | 120 | empty |
| 3 | 840 | 0.86 | 0.90 | 85 | MG, NA, SR |
| 4 | 1068 | 0.86 | 0.88 | 99 | MG, SR, NA |
| 5 | 1085 | 0.86 | 0.88 | 89 | empty |
Interfaces
55 interfaces between chains.
- 0–B · 7410 Ų buried · 228 hydrogen bonds · protein-nucleic
- 0–M · 6492 Ų buried · 168 hydrogen bonds · protein-nucleic
- 0–A · 6278 Ų buried · 172 hydrogen bonds · protein-nucleic
- 0–C · 5593 Ų buried · 139 hydrogen bonds · protein-nucleic
- 0–P · 4352 Ų buried · 127 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 1VQM · The structure of the transition state analogue "DAN" bound to the large ribosomal subunit… · the same entry in another collection · chain M against M, 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 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 1VQM · PDBe 1VQM · UniProt P20276 · 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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