MolNFT v1 · #162495 · protein + DNA
D. melanogaster cmg-DNA, state 1B
6RAX · DNA replication licensing factor MCM2: “D. melanogaster cmg-DNA, state 1B”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.91). MolNFT v1 #162495 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6RAX
- Type
- protein + DNA
- Length
- 5,087 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM2; DNA replication licensing factor MCM3; DNA…
- EC
- 3.6.4.12
- UniProt
- P49735, Q9XYU1, Q26454, Q9VGW6, Q9V461, Q9XYU0, O96989, Q9W0I7, Q9VQY9, Q9W2V7, Q9VBI1
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 13 distinct chains · 30% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 605 | 28% helix, 10% strand | P49735 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 625 | 26% helix, 10% strand | Q9XYU1 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 626 | 27% helix, 11% strand | Q26454 |
| 5 | DNA replication licensing factor MCM5 (EC 3.6.4.12) | protein | 620 | 30% helix, 8% strand | Q9VGW6 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 628 | 27% helix, 6% strand | Q9V461 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 632 | 29% helix, 12% strand | Q9XYU0 |
| X | DNA | dna | 21 | — | — |
| Y | DNA | dna | 8 | — | — |
| A | CDC45L | protein | 567 | 34% helix, 6% strand | O96989 |
| H | IP07275P | protein | 195 | 35% helix, 0% strand | Q9W0I7 |
| L | Probable DNA replication complex gins protein PSF2 | protein | 185 | 40% helix, 5% strand | Q9VQY9 |
| M | AT18545P | protein | 167 | 32% helix, 2% strand | Q9W2V7 |
| N | DNA replication complex gins protein SLD5 | protein | 208 | 45% helix, 2% strand | Q9VBI1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains 2, 6, 3, 5
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains 4, 7, 6, 3
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 | 991 | 0.91 | 0.93 | 140 | empty |
| 2 | 1130 | 0.89 | 0.90 | 151 | ADP |
| 3 | 908 | 0.87 | 0.89 | 93 | empty |
| 4 | 878 | 0.87 | 0.89 | 102 | ATP |
| 5 | 1141 | 0.86 | 0.87 | 119 | empty |
Interfaces
32 interfaces between chains.
- 2–5 · 3612 Ų buried · 32 hydrogen bonds · protein-protein
- 4–6 · 3549 Ų buried · 36 hydrogen bonds · protein-protein
- 3–5 · 3401 Ų buried · 38 hydrogen bonds · protein-protein
- 2–6 · 3398 Ų buried · 36 hydrogen bonds · protein-protein
- 4–7 · 3094 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 6RAX · D. melanogaster CMG-DNA, State 1B · 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 P49735
- Every structure of UniProt Q9XYU1
- Every structure of UniProt Q26454
- Every structure of UniProt Q9VGW6
- Every structure of UniProt Q9V461
- Every structure of UniProt Q9XYU0
- 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
- Elsewhere: RCSB PDB 6RAX · PDBe 6RAX · UniProt P49735 · UniProt Q9XYU1 · UniProt Q26454 · UniProt Q9VGW6 · UniProt Q9V461 · UniProt Q9XYU0 · UniProt O96989 · UniProt Q9W0I7 · UniProt Q9VQY9 · UniProt Q9W2V7 · UniProt Q9VBI1
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