MolNFT v1 · #163173 · protein
Mycoplasma genitalium heterodimer nap complex (P140-P110 globular)
6RUT · Mgp-operon protein 3: “Mycoplasma genitalium heterodimer nap complex (P140-P110 globular)”. X-ray diffraction, 20 pockets (best druggability 0.87). MolNFT v1 #163173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RUT
- Type
- protein
- Length
- 8,157 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mgp-operon protein 3; Adhesin P1
- UniProt
- P22747, P20796
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 17% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mgp-operon protein 3 | protein | 781 | 15% helix, 33% strand | P22747 |
| B | Adhesin P1 | protein | 1268 | 18% helix, 21% strand | P20796 |
| C | Mgp-operon protein 3 | protein | 779 | 15% helix, 32% strand | P22747 |
| D | Adhesin P1 | protein | 1265 | 18% helix, 21% strand | P20796 |
| E | Mgp-operon protein 3 | protein | 783 | 15% helix, 32% strand | P22747 |
| F | Adhesin P1 | protein | 1250 | 18% helix, 21% strand | P20796 |
| G | Mgp-operon protein 3 | protein | 784 | 15% helix, 32% strand | P22747 |
| H | Adhesin P1 | protein | 1247 | 19% helix, 22% strand | P20796 |
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 | 1177 | 0.87 | 0.87 | 129 | empty |
| 2 | 983 | 0.86 | 0.87 | 115 | empty |
| 3 | 427 | 0.85 | 0.93 | 55 | empty |
| 4 | 494 | 0.85 | 0.92 | 65 | empty |
| 5 | 498 | 0.85 | 0.92 | 62 | empty |
Interfaces
13 interfaces between chains.
- E–F · 2952 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2922 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2910 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2851 Ų buried · 33 hydrogen bonds · protein-protein
- E–G · 625 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6RUT · Mycoplasma Genitalium Heterodimer Nap Complex (P140-P110 globular) · the same entry in another collection · chain H against H, TM-score 1.00
- P22747 · AlphaFold monomer V2.0 prediction for mgp-operon protein 3 (P22747) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P20796 · AlphaFold monomer V2.0 prediction for adhesin P1 (P20796) · a predicted model of the same protein · chain F against A, 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 P22747
- Every structure of UniProt P20796
- Elsewhere: RCSB PDB 6RUT · PDBe 6RUT · UniProt P22747 · UniProt P20796
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