MolNFT v1 · #141214 · protein
Mutant (S106A) escherichia COLI L,D-carboxypeptidase a (ldca)
5Z03 · Murein tetrapeptide carboxypeptidase: “Mutant (S106A) escherichia COLI L,D-carboxypeptidase a (ldca)”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT v1 #141214 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5Z03
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Murein tetrapeptide carboxypeptidase
- EC
- 3.4.17.13
- UniProt
- P76008
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Murein tetrapeptide carboxypeptidase (EC 3.4.17.13) | protein | 285 | 35% helix, 23% strand | P76008 |
| B | Murein tetrapeptide carboxypeptidase (EC 3.4.17.13) | protein | 284 | 36% helix, 24% strand | P76008 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.73 | 0.97 | 16 | empty |
| 2 | 160 | 0.46 | 0.76 | 26 | empty |
| 3 | 101 | 0.45 | 0.79 | 20 | empty |
| 4 | 116 | 0.39 | 0.75 | 27 | empty |
| 5 | 59 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1257 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5Z03 · Mutant (S106A) Escherichia coli L,D-carboxypeptidase A (LdcA) · the same entry in another collection · chain A against A, TM-score 1.00
- P76008 · AlphaFold monomer V2.0 prediction for murein tetrapeptide carboxypeptidase (P76008) · 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 P76008
- Elsewhere: RCSB PDB 5Z03 · PDBe 5Z03 · UniProt P76008
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