Research workbench
Structure of apo irtab devoid sid in complex with sybody SYB_NL5
Analyse Structure of apo irtab devoid sid in complex with sybody SYB_NL5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TEJ
- Type
- protein
- Length
- 1,270 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Drug ABC transporter ATP-binding protein; SYB_NL5
- UniProt
- A0A100XEC2, A0A100XE85
- Ligands
- NI
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Drug ABC transporter ATP-binding protein | protein | 561 | 58% helix, 11% strand | A0A100XEC2 |
| B | Drug ABC transporter ATP-binding protein | protein | 585 | 57% helix, 11% strand | A0A100XE85 |
| C | SYB_NL5 | protein | 124 | 2% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.83 | 0.88 | 57 | empty |
| 2 | 577 | 0.80 | 0.85 | 59 | empty |
| 3 | 433 | 0.78 | 0.86 | 46 | empty |
| 4 | 100 | 0.76 | 0.97 | 23 | empty |
| 5 | 397 | 0.71 | 0.82 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–B · 6213 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1003 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6TEJ · Structure of apo IrtAB devoid SID in complex with sybody Syb_NL5 · 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 A0A100XEC2
- Every structure of UniProt A0A100XE85
- Elsewhere: RCSB PDB 6TEJ · PDBe 6TEJ · UniProt A0A100XEC2 · UniProt A0A100XE85
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