Research workbench
Crystal structure of penicillin-binding protein 1 (PBP1) from staphylococcus aureus in complex with pentaglycine
Analyse Crystal structure of penicillin-binding protein 1 (PBP1) from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OK9
- Type
- protein
- Length
- 6,097 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1; Pentaglycine
- UniProt
- A0A0H2WVW5
- Ligands
- CD, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 15 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1 | protein | 522 | 31% helix, 23% strand | A0A0H2WVW5 |
| B | Penicillin-binding protein 1 | protein | 525 | 31% helix, 23% strand | A0A0H2WVW5 |
| C | Penicillin-binding protein 1 | protein | 522 | 31% helix, 23% strand | A0A0H2WVW5 |
| D | Penicillin-binding protein 1 | protein | 496 | 31% helix, 23% strand | A0A0H2WVW5 |
| E | Penicillin-binding protein 1 | protein | 524 | 31% helix, 24% strand | A0A0H2WVW5 |
| F | Penicillin-binding protein 1 | protein | 523 | 32% helix, 24% strand | A0A0H2WVW5 |
| G | Penicillin-binding protein 1 | protein | 520 | 31% helix, 24% strand | A0A0H2WVW5 |
| H | Penicillin-binding protein 1 | protein | 465 | 31% helix, 23% strand | A0A0H2WVW5 |
| I | Penicillin-binding protein 1 | protein | 519 | 31% helix, 23% strand | A0A0H2WVW5 |
| J | Penicillin-binding protein 1 | protein | 518 | 32% helix, 22% strand | A0A0H2WVW5 |
| K | Penicillin-binding protein 1 | protein | 462 | 28% helix, 25% strand | A0A0H2WVW5 |
| L | Penicillin-binding protein 1 | protein | 462 | 31% helix, 25% strand | A0A0H2WVW5 |
| P, Q | Pentaglycine | protein | 5 | 0% helix, 0% strand | — |
| R, S, T, U, V | Pentaglycine | protein | 4 | 0% helix, 0% strand | — |
| W, X, Y | Pentaglycine | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CL · Chloride ion · ion · 3 copies · chains D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 732 | 0.84 | 0.88 | 111 | empty |
| 2 | 1030 | 0.84 | 0.85 | 138 | empty |
| 3 | 1053 | 0.84 | 0.85 | 161 | empty |
| 4 | 721 | 0.83 | 0.87 | 81 | empty |
| 5 | 302 | 0.83 | 0.94 | 48 | empty |
Interfaces
29 interfaces between chains.
- F–I · 2178 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2082 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 1924 Ų buried · 25 hydrogen bonds · protein-protein
- J–L · 1908 Ų buried · 21 hydrogen bonds · protein-protein
- D–H · 1837 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7OK9 · Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in… · the same entry in another collection · chain B against B, 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 A0A0H2WVW5
- Elsewhere: RCSB PDB 7OK9 · PDBe 7OK9 · UniProt A0A0H2WVW5
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