MolNFT v1 · #97387 · protein
Crystal structure of endo-1,5-alpha-L-arabinanase from a bovine ruminal metagenomic library
4KCA: “Crystal structure of endo-1,5-alpha-L-arabinanase from a bovine ruminal metagenomic library”. X-ray diffraction, 2 ligands (NA, IOD), 7 pockets (best druggability 0.73). MolNFT v1 #97387 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KCA
- Type
- protein
- Length
- 1,272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,5-alpha-L-arabinanase
- EC
- 3.2.1.99
- Ligands
- NA, IOD
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,5-alpha-L-arabinanase (EC 3.2.1.99) | protein | 635 | 14% helix, 37% strand | — |
| B | Endo-1,5-alpha-L-arabinanase (EC 3.2.1.99) | protein | 637 | 14% helix, 37% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 63 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.73 | 0.81 | 81 | IOD, GOL |
| 2 | 420 | 0.70 | 0.81 | 61 | GOL, IOD |
| 3 | 366 | 0.64 | 0.79 | 48 | IOD |
| 4 | 294 | 0.62 | 0.79 | 26 | empty |
| 5 | 297 | 0.61 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4KCA · Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic… · 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
- Elsewhere: RCSB PDB 4KCA · PDBe 4KCA
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