MolNFT v1 · #135760 · protein
Crystal structure of beta-lactamase domain protein, from burkholderia multivorans
5U8O · Zn-dependent hydrolase: “Crystal structure of beta-lactamase domain protein, from burkholderia multivorans”. X-ray diffraction, 4 ligands (ZN, CA, UNX), 14 pockets (best druggability 0.85). MolNFT v1 #135760 on GenesisL1: 3D…
- PDB
- 5U8O
- Type
- protein
- Length
- 1,415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zn-dependent hydrolase
- UniProt
- A0A0H3KRR5
- Ligands
- ZN, CA, UNX, CL
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zn-dependent hydrolase | protein | 352 | 36% helix, 24% strand | A0A0H3KRR5 |
| B | Zn-dependent hydrolase | protein | 360 | 36% helix, 24% strand | A0A0H3KRR5 |
| C | Zn-dependent hydrolase | protein | 349 | 36% helix, 24% strand | A0A0H3KRR5 |
| D | Zn-dependent hydrolase | protein | 354 | 36% helix, 24% strand | A0A0H3KRR5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A, B
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.85 | 0.95 | 52 | UNX |
| 2 | 852 | 0.82 | 0.84 | 78 | ZN, UNX |
| 3 | 881 | 0.76 | 0.79 | 70 | UNX |
| 4 | 754 | 0.74 | 0.79 | 57 | UNX |
| 5 | 351 | 0.58 | 0.76 | 45 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1217 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1165 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U8O · Crystal Structure of Beta-lactamase domain protein, from Burkholderia multivorans · 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 A0A0H3KRR5
- Elsewhere: RCSB PDB 5U8O · PDBe 5U8O · UniProt A0A0H3KRR5
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