Research workbench
Virus-like particle of bacteriophage AVE019
Analyse Virus-like particle of bacteriophage AVE019 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YFC
- Type
- protein
- Length
- 21,900 residues
- Chains
- 180
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.246
- Source
- Leviviridae sp.
- Molecule
- coat protein
- Ligands
- CA
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · resolution 3.246 · 2 distinct chains · 21% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AA, AC, AD, AF, AG, AI, AJ, AL, AM, AO, AP, AR, AS, AU, AV, AX, AY, BA, BB, BD, BE, BG, BH, BJ, BK, BM, BN, BP, BQ, BS, BT, BV, BW, BY, BZ, CB, CC, CE, CF, CH, CI, CK, CL, CN, CO, CQ, CR, CT, CU, CW, CX, CZ, DA, DC, DD, DF, DG, DI, DJ, DL, DM, DO, DP, DR, DS, DU, DV, DX, DY, EA, EB, ED, EE, EG, EH, EJ, EK, EM, EN, EP, EQ, ES, ET, EV, EW, EY, EZ, FB, FC, FE, FF, FH, FI, FK, FL, FN, FO, FQ, FR, FT, FU, FW, FX, FZ, GA, GC, GD, GF, GG, GI, GJ, GL, GM, GO, GP, GR, GS, GU, GV, GX | coat protein | protein | 124 | 20% helix, 46% strand | — |
| AB, AE, AH, AK, AN, AQ, AT, AW, AZ, BC, BF, BI, BL, BO, BR, BU, BX, CA, CD, CG, CJ, CM, CP, CS, CV, CY, DB, DE, DH, DK, DN, DQ, DT, DW, DZ, EC, EF, EI, EL, EO, ER, EU, EX, FA, FD, FG, FJ, FM, FP, FS, FV, FY, GB, GE, GH, GK, GN, GQ, GT, GW | coat protein | protein | 117 | 21% helix, 47% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 60 copies · chains AA, AB, AC, BI, DO, FX, AD, AE, AF, BC, DR, GA, AG, AH, AI, BF, DU, GD, AJ, AK, AL, BX, DX, FO, AM, AN, AO, CA, EA, FR, AP, AQ, AR, BU, ED, FU, AS, AT, AU, EG, EL, EZ, AV, AW, AX, EF, EJ, FC, AY, AZ, BA, EI, EM, EW, BB, BD, BR, EP, BE, BG, BL, ES, BH, BJ, BO, EV, BK, BM, DW, EY, BN, BP, DZ, FB, BQ, BS, EC, FE, BT, BV, DN, FH, BW, BY, DQ, FK, BZ, CB, DT, FN, CC, CD, CE, CR, FQ, GK, CF, CG, CH, CL, FT, GN, CI, CJ, CK, CO, FW, GH, CM, CN, DG, FZ, CP, CQ, DJ, GC, CS, CT, DD, GF, CU, CV, CW, DH, GI, GM, CX, CY, CZ, DK, GG, GL, DA, DB, DC, DE, GJ, GO, DF, GR, DI, GU, DL, GX, DM, GT, DP, GW, DS, GQ, DV, GE, DY, FY, EB, GB, EE, EU, EH, EO, EK, ER, EN, FJ, EQ, FM, ET, FG, EX, FI, FA, FL, FD, FF, FP, GV, FS, GP, FV, GS
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 | 227 | 0.63 | 0.82 | 32 | empty |
| 2 | 237 | 0.63 | 0.82 | 35 | empty |
| 3 | 231 | 0.63 | 0.82 | 34 | empty |
| 4 | 233 | 0.63 | 0.82 | 35 | empty |
| 5 | 234 | 0.62 | 0.82 | 35 | empty |
Interfaces
810 interfaces between chains.
- CB–FN · 3578 Ų buried · 47 hydrogen bonds · protein-protein
- BD–EP · 3570 Ų buried · 49 hydrogen bonds · protein-protein
- DC–GO · 3568 Ų buried · 46 hydrogen bonds · protein-protein
- DI–GU · 3566 Ų buried · 45 hydrogen bonds · protein-protein
- BY–FK · 3565 Ų buried · 45 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6YFC · PDBe 6YFC
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