MolNFT v1 · #51996 · protein
Crystal structure of bcla lectin from burkholderia cenocepacia in complex with alpha-methyl-mannoside at 1.7 ångström resolution
2VNV: “Crystal structure of bcla lectin from burkholderia cenocepacia in complex with alpha-methyl-mannoside at 1.7…”. X-ray diffraction, 3 ligands (MMA, CA, SO4), 1 pocket (best druggability 0.74). MolNFT v1 #51996 on GenesisL1: 3D…
- PDB
- 2VNV
- Type
- protein
- Length
- 631 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bcla
- UniProt
- A2W1I5
- Ligands
- MMA, CA, SO4
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bcla | protein | 120 | 3% helix, 58% strand | A2W1I5 |
| B, D, E | Bcla | protein | 128 | 5% helix, 55% strand | A2W1I5 |
| C | Bcla | protein | 127 | 2% helix, 55% strand | A2W1I5 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 5 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.74 | 0.78 | 52 | MMA |
Interfaces
5 interfaces between chains.
- A–B · 1543 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1516 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 87 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VNV · Crystal structure of BclA lectin from burkholderia cenocepacia in complex with… · 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 A2W1I5
- Elsewhere: RCSB PDB 2VNV · PDBe 2VNV · UniProt A2W1I5
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