MolNFT v1 · #170016 · protein + DNA
Cryoem structure of human cmg bound to atpgammas and DNA
6XTX · DNA replication licensing factor MCM2: “Cryoem structure of human cmg bound to atpgammas and DNA”. Electron microscopy, 4 ligands (AGS, ADP, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #170016 on GenesisL1: 3D structure…
- PDB
- 6XTX
- Type
- protein + DNA
- Length
- 5,069 residues
- Chains
- 12
- 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
- P49736, P25205, P33991, P33992, Q14566, P33993, Q14691, Q9Y248, Q9BRX5, Q9BRT9, O75419
- Ligands
- AGS, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 12 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 691 | 36% helix, 15% strand | P49736 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 608 | 29% helix, 17% strand | P25205 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 598 | 30% helix, 16% strand | P33991 |
| 5 | DNA replication licensing factor MCM5 (EC 3.6.4.12) | protein | 577 | 35% helix, 23% strand | P33992 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 679 | 33% helix, 18% strand | Q14566 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 598 | 31% helix, 21% strand | P33993 |
| A | DNA replication complex gins protein PSF1 | protein | 196 | 46% helix, 8% strand | Q14691 |
| B | DNA replication complex gins protein PSF2 | protein | 176 | 48% helix, 10% strand | Q9Y248 |
| C | DNA replication complex gins protein PSF3 | protein | 194 | 35% helix, 7% strand | Q9BRX5 |
| D | DNA replication complex gins protein SLD5 | protein | 203 | 45% helix, 12% strand | Q9BRT9 |
| E | Cell division control protein 45 homolog | protein | 538 | 39% helix, 14% strand | O75419 |
| M | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains 4, 7, 6, 3
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 2, 6, 3, 5
- ZN · Zinc ion · metal · 5 copies · chains 2, 4, 5, 6, 7
- MG · Magnesium ion · metal · 3 copies · chains 4, 6, 3, 7
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 | 947 | 0.87 | 0.88 | 98 | empty |
| 2 | 296 | 0.85 | 0.95 | 41 | empty |
| 3 | 917 | 0.85 | 0.86 | 118 | empty |
| 4 | 993 | 0.85 | 0.86 | 108 | empty |
| 5 | 1086 | 0.84 | 0.85 | 103 | ADP |
Interfaces
29 interfaces between chains.
- 2–6 · 3850 Ų buried · 25 hydrogen bonds · protein-protein
- 4–7 · 3719 Ų buried · 20 hydrogen bonds · protein-protein
- 4–6 · 3669 Ų buried · 18 hydrogen bonds · protein-protein
- 3–7 · 3455 Ų buried · 24 hydrogen bonds · protein-protein
- 3–5 · 3422 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6XTX · CryoEM structure of human CMG bound to ATPgammaS and DNA · the same entry in another collection · chain M against M, 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 P49736
- Every structure of UniProt P25205
- Every structure of UniProt P33991
- Every structure of UniProt P33992
- Every structure of UniProt Q14566
- Every structure of UniProt P33993
- Every structure of UniProt Q14691
- Every structure of UniProt Q9Y248
- Every structure of UniProt Q9BRX5
- Every structure of UniProt Q9BRT9
- Every structure of UniProt O75419
- Elsewhere: RCSB PDB 6XTX · PDBe 6XTX · UniProt P49736 · UniProt P25205 · UniProt P33991 · UniProt P33992 · UniProt Q14566 · UniProt P33993 · UniProt Q14691 · UniProt Q9Y248 · UniProt Q9BRX5 · UniProt Q9BRT9 · UniProt O75419
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