MolNFT v1 · #144531 · protein
Crystal structure of mycoibacterium tuberculosis RV2983 in complex with pep
6BWH · 2-phospho-L-lactate guanylyltransferase: “Crystal structure of mycoibacterium tuberculosis RV2983 in complex with pep”. X-ray diffraction, 2 ligands (PEP, MG), 6 pockets (best druggability 0.68). MolNFT v1 #144531 on GenesisL1: 3D…
- PDB
- 6BWH
- Type
- protein
- Length
- 614 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-phospho-L-lactate guanylyltransferase
- EC
- 2.7.7.68
- UniProt
- P9WP83
- Ligands
- PEP, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-phospho-L-lactate guanylyltransferase (EC 2.7.7.68) | protein | 207 | 42% helix, 18% strand | P9WP83 |
| C | 2-phospho-L-lactate guanylyltransferase (EC 2.7.7.68) | protein | 200 | 44% helix, 19% strand | P9WP83 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.68 | 0.76 | 74 | empty |
| 2 | 333 | 0.63 | 0.79 | 44 | PEP, MG |
| 3 | 245 | 0.63 | 0.81 | 25 | PEP |
| 4 | 192 | 0.60 | 0.82 | 30 | PEP, MG |
| 5 | 179 | 0.47 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 688 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 281 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 6BWH · Crystal structure of Mycoibacterium tuberculosis Rv2983 in complex with PEP · the same entry in another collection · chain A against A, TM-score 1.00
- P9WP83 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate guanylyltransferase (P9WP83) · a predicted model of the same protein · chain A 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 P9WP83
- Elsewhere: RCSB PDB 6BWH · PDBe 6BWH · UniProt P9WP83
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