MolNFT v1 · #124078 · protein
Directed evolutionary changes in mbl super family - ndm-1 round 10 crystal-3
5K4M · Metallo-beta-lactamase type 2: “Directed evolutionary changes in mbl super family - ndm-1 round 10 crystal-3”. X-ray diffraction, 4 ligands (SV7, NPO, ZN), 1 pocket (best druggability 0.43). MolNFT v1 #124078 on GenesisL1: 3D…
- PDB
- 5K4M
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- SV7, NPO, ZN, MG
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 228 | 28% helix, 27% strand | C7C422 |
Ligands and binding sites
- SV7 · phenylphosphonic acid · ligand · 2 copies · chains A
- NPO · P-nitrophenol · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.43 | 0.74 | 21 | SV7 |
Compared structures
- 5K4M · Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-3 · the same entry in another collection · chain A against A, TM-score 1.00
- C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 C7C422
- Elsewhere: RCSB PDB 5K4M · PDBe 5K4M · UniProt C7C422
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