MolNFT v1 · #150109 · protein
Structure of xiap-BIR1 domain in complex with an NF023 analog
6GJW · E3 ubiquitin-protein ligase xiap: “Structure of xiap-BIR1 domain in complex with an NF023 analog”. X-ray diffraction, 2 ligands (F2H, ZN), 3 pockets (best druggability 0.38). MolNFT v1 #150109 on GenesisL1: 3D structure, binding…
- PDB
- 6GJW
- Type
- protein
- Length
- 312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap
- EC
- 2.3.2.27
- UniProt
- P98170
- Ligands
- F2H, ZN
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 78 | 32% helix, 10% strand | P98170 |
Ligands and binding sites
- F2H · 4-[[3-[[3-[(4,8-disulfonatonaphthalen-1-yl) carbamoyl]phenyl]carbamoylamino]phenyl]carbonylamino]n aphthalene-1,5-disulfonate · ligand · 2 copies · chains B, C, A, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.38 | 0.79 | 13 | empty |
| 2 | 56 | 0.29 | 0.75 | 16 | empty |
| 3 | 59 | 0.28 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 592 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 580 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 372 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GJW · Structure of XIAP-BIR1 domain in complex with an NF023 analog · 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 P98170
- Elsewhere: RCSB PDB 6GJW · PDBe 6GJW · UniProt P98170
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