MolNFT v1 · #52564 · protein
Human dcmp deaminase
2W4L · Deoxycytidylate deaminase: “Human dcmp deaminase”. X-ray diffraction, 2 ligands (ZN, CL), 11 pockets (best druggability 0.76). MolNFT v1 #52564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2W4L
- Type
- protein
- Length
- 930 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidylate deaminase
- EC
- 3.5.4.12
- UniProt
- P32321
- Ligands
- ZN, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidylate deaminase (EC 3.5.4.12) | protein | 160 | 30% helix, 21% strand | P32321 |
| B | Deoxycytidylate deaminase (EC 3.5.4.12) | protein | 157 | 32% helix, 22% strand | P32321 |
| C | Deoxycytidylate deaminase (EC 3.5.4.12) | protein | 142 | 32% helix, 24% strand | P32321 |
| D | Deoxycytidylate deaminase (EC 3.5.4.12) | protein | 150 | 35% helix, 23% strand | P32321 |
| E | Deoxycytidylate deaminase (EC 3.5.4.12) | protein | 162 | 30% helix, 21% strand | P32321 |
| F | Deoxycytidylate deaminase (EC 3.5.4.12) | protein | 159 | 31% helix, 21% strand | P32321 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.76 | 0.78 | 107 | empty |
| 2 | 892 | 0.75 | 0.79 | 105 | CL |
| 3 | 821 | 0.74 | 0.78 | 96 | CL |
| 4 | 497 | 0.68 | 0.79 | 68 | empty |
| 5 | 237 | 0.62 | 0.81 | 40 | empty |
Interfaces
10 interfaces between chains.
- A–F · 2415 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2039 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1989 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1434 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1390 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 P32321
- Elsewhere: RCSB PDB 2W4L · PDBe 2W4L · UniProt P32321
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