MolNFT v1 · #163270 · protein
Crystal structure of cobb AC2 (A76G, I131C, V162G) in complex with H4K16CR-2'OH-adpr peptide intermediate after co-crystallisation
6RXR · NAD-dependent protein deacylase: “Crystal structure of cobb AC2 (A76G, I131C, V162G) in complex with H4K16CR-2'OH-adpr peptide intermediate…”. X-ray diffraction, 1 ligand (KMQ), 12 pockets (best druggability 0.81). MolNFT v1 #163270…
- PDB
- 6RXR
- Type
- protein
- Length
- 937 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase; Histone H4
- EC
- 3.5.1.-
- UniProt
- P75960, P02309
- Ligands
- KMQ
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 224 | 41% helix, 22% strand | P75960 |
| B | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 226 | 40% helix, 22% strand | P75960 |
| C | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 225 | 40% helix, 22% strand | P75960 |
| D | NAD-dependent protein deacylase (EC 3.5.1.-) | protein | 226 | 40% helix, 22% strand | P75960 |
| E, G | Histone H4 | protein | 9 | 0% helix, 22% strand | P02309 |
| F | Histone H4 | protein | 10 | 0% helix, 20% strand | P02309 |
| H | Histone H4 | protein | 8 | 0% helix, 25% strand | P02309 |
Ligands and binding sites
- KMQ · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.81 | 0.86 | 74 | KMQ |
| 2 | 528 | 0.80 | 0.86 | 60 | KMQ |
| 3 | 557 | 0.79 | 0.85 | 64 | KMQ |
| 4 | 536 | 0.78 | 0.85 | 61 | KMQ |
| 5 | 150 | 0.53 | 0.80 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–D · 639 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 529 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 520 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 518 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 508 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6RXR · Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr… · the same entry in another collection · chain H against H, TM-score 1.00
- P75960 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase (P75960) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P75960
- Every structure of UniProt P02309
- Elsewhere: RCSB PDB 6RXR · PDBe 6RXR · UniProt P75960 · UniProt P02309
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