MolNFT v1 · #119325 · protein
Crystal structure of penicillin binding protein 6B from escherichia COLI
5FSR · D-alanyl-D-alanine carboxypeptidase dacd: “Crystal structure of penicillin binding protein 6B from escherichia COLI”. X-ray diffraction, 3 pockets (best druggability 0.76). MolNFT v1 #119325 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FSR
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase dacd
- EC
- 3.4.16.4
- UniProt
- P33013
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase dacd (EC 3.4.16.4) | protein | 318 | 32% helix, 27% strand | P33013 |
| B | D-alanyl-D-alanine carboxypeptidase dacd (EC 3.4.16.4) | protein | 317 | 32% helix, 28% strand | P33013 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.76 | 0.80 | 92 | empty |
| 2 | 216 | 0.67 | 0.85 | 34 | empty |
| 3 | 54 | 0.28 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 778 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5FSR · Crystal structure of penicillin binding protein 6B from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P33013 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacd (P33013) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P33013
- Elsewhere: RCSB PDB 5FSR · PDBe 5FSR · UniProt P33013
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