MolNFT v1 · #67155 · protein
Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from haemophilus influenzae
3IC1: “Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from haemophilus influenzae”. X-ray diffraction, 2 ligands (ZN, SO4), 3 pockets (best druggability 0.60). MolNFT v1 #67155 on GenesisL1: 3D structure, binding…
- PDB
- 3IC1
- Type
- protein
- Length
- 739 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-diaminopimelate desuccinylase
- EC
- 3.5.1.18
- UniProt
- P44514
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 370 | 34% helix, 26% strand | P44514 |
| B | Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) | protein | 369 | 33% helix, 26% strand | P44514 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.60 | 0.77 | 55 | SO4 |
| 2 | 68 | 0.37 | 0.79 | 17 | empty |
| 3 | 91 | 0.37 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1104 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3IC1 · Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus… · the same entry in another collection · chain A against A, TM-score 1.00
- P44514 · AlphaFold monomer V2.0 prediction for succinyl-diaminopimelate desuccinylase (P44514) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P44514
- Elsewhere: RCSB PDB 3IC1 · PDBe 3IC1 · UniProt P44514
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