MolNFT v1 · #107083 · protein + DNA
Crystal structure of canavalia maritima lectin (conm) complexed with interleukin - 1 beta primer
4TZD · Concanavalin-a: “Crystal structure of canavalia maritima lectin (conm) complexed with interleukin - 1 beta primer”. X-ray diffraction, 3 pockets (best druggability 0.45). MolNFT v1 #107083 on GenesisL1: 3D structure, binding sites…
- PDB
- 4TZD
- Type
- protein + DNA
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-a; DNA (5'-D(P*CP*G)-3'); DNA (5'-D(P*TP*C)-3')
- UniProt
- P81460
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Concanavalin-a | protein | 232 | 4% helix, 43% strand | P81460 |
| G | DNA (5'-D(P*CP*G)-3') | dna | 2 | — | — |
| H | DNA (5'-D(P*TP*C)-3') | dna | 2 | — | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.45 | 0.78 | 26 | empty |
| 2 | 73 | 0.35 | 0.77 | 14 | empty |
| 3 | 71 | 0.34 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 717 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 273 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–H · 237 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–G · 236 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–H · 205 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4TZD · Crystal structure of Canavalia maritima lectin (ConM) complexed with interleukin - 1 beta… · the same entry in another collection · chain A against A, TM-score 1.00
- P81460 · AlphaFold monomer V2.0 prediction for concanavalin-a (P81460) · a predicted model of the same protein · chain D 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 P81460
- Elsewhere: RCSB PDB 4TZD · PDBe 4TZD · UniProt P81460
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