Research workbench
D. melanogaster cmg-DNA, state 2A
Analyse D. melanogaster cmg-DNA, state 2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAY
- Type
- protein + DNA
- Length
- 4,900 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM3; DNA replication licensing factor MCM4; DNA…
- EC
- 3.6.4.12
- UniProt
- Q9XYU1, Q26454, Q9XYU0, Q9V461, Q9VGW6, O96989, Q9W0I7, Q9VQY9, Q9W2V7, Q9VBI1, P49735
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 12 distinct chains · 29% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 600 | 28% helix, 10% strand | Q9XYU1 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 617 | 27% helix, 10% strand | Q26454 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 587 | 30% helix, 7% strand | Q9XYU0 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 600 | 27% helix, 7% strand | Q9V461 |
| 5 | DNA replication licensing factor MCM5 (EC 3.6.4.12) | protein | 577 | 25% helix, 8% strand | Q9VGW6 |
| A | CDC45L | protein | 567 | 32% helix, 7% strand | O96989 |
| H | IP07275P | protein | 189 | 37% helix, 1% strand | Q9W0I7 |
| L | Probable DNA replication complex gins protein PSF2 | protein | 177 | 36% helix, 5% strand | Q9VQY9 |
| M | AT18545P | protein | 167 | 28% helix, 2% strand | Q9W2V7 |
| N | DNA replication complex gins protein SLD5 | protein | 206 | 39% helix, 2% strand | Q9VBI1 |
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 600 | 28% helix, 8% strand | P49735 |
| X | DNA (5'-D(P*AP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains 3, 5, 4, 7, 6, 2
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 3, 7, 5, 2
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 | 949 | 0.89 | 0.91 | 117 | ATP |
| 2 | 683 | 0.89 | 0.93 | 122 | empty |
| 3 | 730 | 0.88 | 0.92 | 105 | ATP |
| 4 | 757 | 0.88 | 0.91 | 85 | empty |
| 5 | 753 | 0.88 | 0.91 | 115 | empty |
Interfaces
28 interfaces between chains.
- 4–6 · 3725 Ų buried · 49 hydrogen bonds · protein-protein
- 4–7 · 3399 Ų buried · 37 hydrogen bonds · protein-protein
- 3–5 · 2992 Ų buried · 19 hydrogen bonds · protein-protein
- 6–2 · 2871 Ų buried · 27 hydrogen bonds · protein-protein
- 5–2 · 2761 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6RAY · D. melanogaster CMG-DNA, State 2A · the same entry in another collection · chain N against N, 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 Q9XYU1
- Every structure of UniProt Q26454
- Every structure of UniProt Q9XYU0
- Every structure of UniProt Q9V461
- Every structure of UniProt Q9VGW6
- 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
- Elsewhere: RCSB PDB 6RAY · PDBe 6RAY · UniProt Q9XYU1 · UniProt Q26454 · UniProt Q9XYU0 · UniProt Q9V461 · UniProt Q9VGW6 · UniProt O96989 · UniProt Q9W0I7 · UniProt Q9VQY9 · UniProt Q9W2V7 · UniProt Q9VBI1 · UniProt P49735
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