MolNFT v1 · #106004 · protein
Structural and mechanistic insights into ndm-1 catalyzed hydrolysis of cephalosporins
4RM5 · Beta-lactamase ndm-1: “Structural and mechanistic insights into ndm-1 catalyzed hydrolysis of cephalosporins”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.77). MolNFT v1 #106004 on GenesisL1: 3D structure…
- PDB
- 4RM5
- Type
- protein
- Length
- 894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ndm-1
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 226 | 24% helix, 31% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 222 | 27% helix, 29% strand | C7C422 |
| C | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 223 | 25% helix, 30% strand | C7C422 |
| D | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 223 | 26% helix, 30% strand | C7C422 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.77 | 0.97 | 21 | empty |
| 2 | 1188 | 0.76 | 0.79 | 85 | ZN |
| 3 | 332 | 0.57 | 0.76 | 49 | ZN |
| 4 | 61 | 0.29 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1041 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 324 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 244 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 168 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RM5 · Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins · the same entry in another collection · chain D against D, 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 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 C7C422
- Elsewhere: RCSB PDB 4RM5 · PDBe 4RM5 · UniProt C7C422
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