MolNFT v1 · #111654 · protein
Complex of SPAO(SPOA1,2 semet) and ORGB(APAR)::T4LYSOZYME fusion protein
4YXA · Surface presentation of antigens protein spao: “Complex of SPAO(SPOA1,2 semet) and ORGB(APAR)::T4LYSOZYME fusion protein”. X-ray diffraction, 12 pockets (best druggability 0.66). MolNFT v1 #111654 on GenesisL1: 3D structure, binding…
- PDB
- 4YXA
- Type
- protein
- Length
- 618 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface presentation of antigens protein spao; Oxygen-regulated invasion protein…
- EC
- 3.2.1.17
- UniProt
- P40699, P0CL45, P00720
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Surface presentation of antigens protein spao | protein | 62 | 0% helix, 60% strand | P40699 |
| B | Surface presentation of antigens protein spao | protein | 67 | 15% helix, 57% strand | P40699 |
| C | Oxygen-regulated invasion protein ORGB,ENDOLYSIN (EC 3.2.1.17) | protein | 168 | 58% helix, 7% strand | P0CL45, P00720 |
| E | Surface presentation of antigens protein spao | protein | 66 | 17% helix, 61% strand | P40699 |
| F | Oxygen-regulated invasion protein ORGB,ENDOLYSIN (EC 3.2.1.17) | protein | 193 | 56% helix, 8% strand | P0CL45, P00720 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.66 | 0.78 | 59 | empty |
| 2 | 264 | 0.58 | 0.78 | 34 | empty |
| 3 | 52 | 0.56 | 0.90 | 16 | empty |
| 4 | 62 | 0.51 | 0.86 | 20 | empty |
| 5 | 107 | 0.49 | 0.80 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1899 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 1856 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 594 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 534 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4YXA · Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein · the same entry in another collection · chain F against F, TM-score 1.00
- P40699 · AlphaFold monomer V2.0 prediction for surface presentation of antigens protein spao… · a predicted model of the same protein · chain E against A, TM-score 0.91
- P0CL45 · AlphaFold monomer V2.0 prediction for spi-1 type 3 secretion system stator protein… · a predicted model of the same protein · chain C against A, TM-score 0.24
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 P40699
- Every structure of UniProt P0CL45
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 4YXA · PDBe 4YXA · UniProt P40699 · UniProt P0CL45 · UniProt P00720
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