MolNFT v1 · #109767 · protein
S-ribosylhomocysteinase from streptococcus suis
4XCH · S-ribosylhomocysteine lyase: “S-ribosylhomocysteinase from streptococcus suis”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.63). MolNFT v1 #109767 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XCH
- Type
- protein
- Length
- 596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-ribosylhomocysteine lyase
- EC
- 4.4.1.21
- UniProt
- B2CMA5
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | S-ribosylhomocysteine lyase (EC 4.4.1.21) | protein | 149 | 34% helix, 21% strand | B2CMA5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.63 | 0.79 | 31 | empty |
| 2 | 338 | 0.63 | 0.79 | 29 | ZN |
| 3 | 343 | 0.62 | 0.78 | 29 | empty |
| 4 | 335 | 0.61 | 0.78 | 30 | empty |
| 5 | 58 | 0.30 | 0.75 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1621 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 618 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 164 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4XCH · S-ribosylhomocysteinase from Streptococcus suis · the same entry in another collection · chain B against B, 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 B2CMA5
- Elsewhere: RCSB PDB 4XCH · PDBe 4XCH · UniProt B2CMA5
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