MolNFT v1 · #117026 · protein
2.95 ångström crystal structure of the dimeric form of penicillin binding protein 2 prime from enterococcus faecium
5DVY: “2.95 ångström crystal structure of the dimeric form of penicillin binding protein 2 prime from enterococcus…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.52). MolNFT v1 #117026 on GenesisL1: 3D structure…
- PDB
- 5DVY
- Type
- protein
- Length
- 641 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin binding protein 2 prime
- UniProt
- Q3XZN6
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin binding protein 2 prime | protein | 641 | 33% helix, 26% strand | Q3XZN6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.52 | 0.80 | 29 | empty |
| 2 | 225 | 0.48 | 0.74 | 27 | empty |
| 3 | 155 | 0.42 | 0.75 | 28 | empty |
| 4 | 54 | 0.38 | 0.80 | 16 | empty |
| 5 | 66 | 0.33 | 0.75 | 19 | SO4 |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 5DVY · 2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime… · 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 Q3XZN6
- Elsewhere: RCSB PDB 5DVY · PDBe 5DVY · UniProt Q3XZN6
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