MolNFT v1 · #100318 · protein
Structure of xiap-BIR1 in complex with NF023
4MTZ · E3 ubiquitin-protein ligase xiap: “Structure of xiap-BIR1 in complex with NF023”. X-ray diffraction, 3 ligands (0BU, ZN, SO4), 5 pockets (best druggability 0.41). MolNFT v1 #100318 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4MTZ
- Type
- protein
- Length
- 309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap
- EC
- 6.3.2.-
- UniProt
- P98170
- Ligands
- 0BU, ZN, SO4
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 78 | 28% helix, 10% strand | P98170 |
| B, C, D | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 77 | 26% helix, 10% strand | P98170 |
Ligands and binding sites
- 0BU · 8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.41 | 0.81 | 16 | empty |
| 2 | 62 | 0.35 | 0.78 | 18 | empty |
| 3 | 51 | 0.33 | 0.78 | 19 | empty |
| 4 | 67 | 0.28 | 0.73 | 21 | empty |
| 5 | 54 | 0.25 | 0.72 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 575 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 567 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 103 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MTZ · Structure of XIAP-BIR1 in complex with NF023 · 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 4MTZ · PDBe 4MTZ · UniProt P98170
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