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Crystal structure of the DIP2311 protein from corynebacterium diphtheriae, northeast structural genomics consortium target CDR35
Analyse Crystal structure of the DIP2311 protein from corynebacterium diphtheriae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMM
- Type
- protein
- Length
- 2,080 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q6NEG3
- Ligands
- CO, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 492 | 39% helix, 21% strand | Q6NEG3 |
| B | Uncharacterized protein | protein | 555 | 41% helix, 18% strand | Q6NEG3 |
| C | Uncharacterized protein | protein | 477 | 39% helix, 20% strand | Q6NEG3 |
| D | Uncharacterized protein | protein | 556 | 40% helix, 19% strand | Q6NEG3 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.84 | 0.85 | 103 | empty |
| 2 | 1166 | 0.83 | 0.84 | 111 | empty |
| 3 | 214 | 0.81 | 0.95 | 28 | empty |
| 4 | 169 | 0.80 | 0.95 | 26 | empty |
| 5 | 175 | 0.79 | 0.94 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1593 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1581 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1058 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 3LMM · Crystal Structure of the DIP2311 protein from Corynebacterium diphtheriae, Northeast… · the same entry in another collection · chain A against A, 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 Q6NEG3
- Elsewhere: RCSB PDB 3LMM · PDBe 3LMM · UniProt Q6NEG3
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