MolNFT v1 · #188292 · protein
1.95A resolution structure of independent phosphoglycerate mutase from S. aureus in complex with a macrocyclic peptide inhibitor (sa-D3)
7TL8 · 2,3-bisphosphoglycerate-independent phosphoglycerate mutase: “1.95A resolution structure of independent phosphoglycerate mutase from S. aureus in complex with a…”. X-ray diffraction, 2 ligands (ACE, MN), 4 pockets (best druggability…
- PDB
- 7TL8
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Peptide sa-D3
- EC
- 5.4.2.12
- UniProt
- W8U5L7
- Ligands
- ACE, MN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 488 | 40% helix, 15% strand | W8U5L7 |
| B | Peptide sa-D3 | protein | 14 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.51 | 0.85 | 17 | empty |
| 2 | 163 | 0.47 | 0.76 | 23 | empty |
| 3 | 173 | 0.42 | 0.73 | 30 | MN |
| 4 | 63 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 921 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 7TL8 · 1.95A resolution structure of independent phosphoglycerate mutase from S. aureus in… · the same entry in another collection · 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 W8U5L7
- Elsewhere: RCSB PDB 7TL8 · PDBe 7TL8 · UniProt W8U5L7
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