MolNFT v1 · #127238 · protein
Glycoside hydrolase BT_1002
5MQP: “Glycoside hydrolase BT_1002”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.82). MolNFT v1 #127238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MQP
- Type
- protein
- Length
- 4,801 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase BT_1002
- UniProt
- A0A0P0F5L7
- Ligands
- CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, H | Glycoside hydrolase BT_1002 | protein | 600 | 10% helix, 42% strand | A0A0P0F5L7 |
| B, F | Glycoside hydrolase BT_1002 | protein | 599 | 9% helix, 42% strand | A0A0P0F5L7 |
| C | Glycoside hydrolase BT_1002 | protein | 601 | 10% helix, 42% strand | A0A0P0F5L7 |
| E | Glycoside hydrolase BT_1002 | protein | 602 | 10% helix, 41% strand | A0A0P0F5L7 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.82 | 0.83 | 90 | empty |
| 2 | 1035 | 0.82 | 0.83 | 92 | empty |
| 3 | 1065 | 0.82 | 0.83 | 90 | empty |
| 4 | 961 | 0.81 | 0.83 | 91 | empty |
| 5 | 771 | 0.77 | 0.81 | 99 | empty |
Interfaces
9 interfaces between chains.
- G–H · 2572 Ų buried · 44 hydrogen bonds · protein-protein
- B–F · 2560 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2548 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 2547 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 888 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5MQP · Glycoside hydrolase BT_1002 · 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 A0A0P0F5L7
- Elsewhere: RCSB PDB 5MQP · PDBe 5MQP · UniProt A0A0P0F5L7
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