Research workbench
D. melanogaster cmg-DNA, state 2B
Analyse D. melanogaster cmg-DNA, state 2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAZ
- Type
- protein + DNA
- Length
- 4,787 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA; CDC45L; IP07275P; Probable DNA replication complex gins protein PSF2; AT18545P; DNA…
- EC
- 3.6.4.12
- UniProt
- O96989, Q9W0I7, Q9VQY9, Q9W2V7, Q9VBI1, P49735, Q9VGW6, Q9V461, Q9XYU1, Q26454, Q9XYU0
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 13 distinct chains · 30% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | DNA | dna | 21 | — | — |
| Y | DNA | dna | 2 | — | — |
| A | CDC45L | protein | 519 | 38% helix, 6% strand | O96989 |
| H | IP07275P | protein | 195 | 38% helix, 0% strand | Q9W0I7 |
| L | Probable DNA replication complex gins protein PSF2 | protein | 179 | 33% helix, 6% strand | Q9VQY9 |
| M | AT18545P | protein | 150 | 33% helix, 3% strand | Q9W2V7 |
| N | DNA replication complex gins protein SLD5 | protein | 206 | 46% helix, 2% strand | Q9VBI1 |
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 559 | 30% helix, 8% strand | P49735 |
| 5 | DNA replication licensing factor MCM5 (EC 3.6.4.12) | protein | 571 | 24% helix, 7% strand | Q9VGW6 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 588 | 28% helix, 6% strand | Q9V461 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 590 | 24% helix, 11% strand | Q9XYU1 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 606 | 24% helix, 10% strand | Q26454 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 601 | 31% helix, 15% strand | Q9XYU0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains 6, 4, 5, 3, 7
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 2, 5, 6
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 | 1000 | 0.89 | 0.91 | 139 | ATP |
| 2 | 794 | 0.89 | 0.93 | 125 | ATP |
| 3 | 783 | 0.89 | 0.93 | 131 | empty |
| 4 | 740 | 0.88 | 0.92 | 120 | ATP |
| 5 | 759 | 0.88 | 0.91 | 101 | empty |
Interfaces
28 interfaces between chains.
- 4–7 · 3477 Ų buried · 40 hydrogen bonds · protein-protein
- 2–5 · 3172 Ų buried · 42 hydrogen bonds · protein-protein
- 6–4 · 3075 Ų buried · 41 hydrogen bonds · protein-protein
- 3–7 · 2892 Ų buried · 28 hydrogen bonds · protein-protein
- 5–3 · 2560 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6RAZ · D. melanogaster CMG-DNA, State 2B · the same entry in another collection · chain 7 against 7, 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 O96989
- Every structure of UniProt Q9W0I7
- Every structure of UniProt Q9VQY9
- Every structure of UniProt Q9W2V7
- Every structure of UniProt Q9VBI1
- Every structure of UniProt P49735
- Every structure of UniProt Q9VGW6
- Every structure of UniProt Q9V461
- Every structure of UniProt Q9XYU1
- Every structure of UniProt Q26454
- Every structure of UniProt Q9XYU0
- Elsewhere: RCSB PDB 6RAZ · PDBe 6RAZ · UniProt O96989 · UniProt Q9W0I7 · UniProt Q9VQY9 · UniProt Q9W2V7 · UniProt Q9VBI1 · UniProt P49735 · UniProt Q9VGW6 · UniProt Q9V461 · UniProt Q9XYU1 · UniProt Q26454 · UniProt Q9XYU0
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