MolNFT v1 · #52760 · protein
Penicillin-binding protein 2B (pbp-2B) from streptococcus pneumoniae (strain 5204)
2WAD: “Penicillin-binding protein 2B (pbp-2B) from streptococcus pneumoniae (strain 5204)”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.72). MolNFT v1 #52760 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2WAD
- Type
- protein
- Length
- 1,818 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2B
- EC
- 3.4.-.-
- UniProt
- P0A3M6
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2B (EC 3.4.-.-) | protein | 606 | 35% helix, 21% strand | P0A3M6 |
| B | Penicillin-binding protein 2B (EC 3.4.-.-) | protein | 605 | 34% helix, 21% strand | P0A3M6 |
| C | Penicillin-binding protein 2B (EC 3.4.-.-) | protein | 607 | 35% helix, 21% strand | P0A3M6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.72 | 0.76 | 104 | empty |
| 2 | 389 | 0.68 | 0.81 | 57 | empty |
| 3 | 435 | 0.64 | 0.78 | 53 | empty |
| 4 | 371 | 0.62 | 0.78 | 39 | empty |
| 5 | 230 | 0.50 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 249 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 230 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2WAD · Penicillin-binding protein 2B (pbp-2B) from streptococcus pneumoniae (strain 5204) · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3M6 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2B (P0A3M6) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0A3M6
- Elsewhere: RCSB PDB 2WAD · PDBe 2WAD · UniProt P0A3M6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.