MolNFT v1 · #126160 · protein
Crystal structure of human spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide
5LUG · Spindlin-like protein 2, isoform CRA_A: “Crystal structure of human spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide”. X-ray diffraction, 1 ligand (2MR), 15 pockets (best druggability 0.83). MolNFT v1 #126160 on…
- PDB
- 5LUG
- Type
- protein
- Length
- 854 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-like protein 2, isoform CRA_A; Ala-arg-thr-M3L-gln-thr-ala-2MR-lys-ser
- UniProt
- A0A024R9Y9
- Ligands
- 2MR
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spindlin-like protein 2, isoform CRA_A | protein | 207 | 8% helix, 45% strand | A0A024R9Y9 |
| C | Spindlin-like protein 2, isoform CRA_A | protein | 205 | 10% helix, 45% strand | A0A024R9Y9 |
| D | Spindlin-like protein 2, isoform CRA_A | protein | 204 | 9% helix, 45% strand | A0A024R9Y9 |
| F, G, H | Ala-arg-thr-M3L-gln-thr-ala-2MR-lys-ser | protein | 8 | 0% helix, 13% strand | — |
| E | Ala-arg-thr-M3L-gln-thr-ala-2MR-lys-ser | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- 2MR · N3, N4-dimethylarginine · ligand · chains B, E
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, F, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.83 | 0.84 | 78 | empty |
| 2 | 1148 | 0.81 | 0.82 | 77 | empty |
| 3 | 407 | 0.68 | 0.81 | 48 | empty |
| 4 | 184 | 0.58 | 0.81 | 29 | empty |
| 5 | 94 | 0.49 | 0.82 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–C · 901 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 878 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 665 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 655 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 651 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (methylation).
Compared structures
- 5LUG · Crystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide · 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 A0A024R9Y9
- Elsewhere: RCSB PDB 5LUG · PDBe 5LUG · UniProt A0A024R9Y9
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