Research workbench
Cryoem structure of human cmg bound to and-1 (cmga)
Analyse Cryoem structure of human cmg bound to and-1 (cmga) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XTY
- Type
- protein
- Length
- 6,117 residues
- Chains
- 14
- 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, O75717
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 12 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 611 | 36% helix, 17% 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, 15% 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 | 609 | 31% helix, 20% strand | Q14566 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 598 | 31% helix, 20% 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 |
| F, G, H | Wd repeat and hmg-box DNA-binding protein 1 | protein | 403 | 23% helix, 35% strand | O75717 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains 2, 4, 5, 6, 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 | 931 | 0.89 | 0.91 | 113 | empty |
| 2 | 1012 | 0.86 | 0.87 | 129 | empty |
| 3 | 917 | 0.85 | 0.87 | 102 | empty |
| 4 | 331 | 0.85 | 0.94 | 52 | empty |
| 5 | 1123 | 0.84 | 0.85 | 128 | empty |
Interfaces
27 interfaces between chains.
- 3–7 · 3503 Ų buried · 27 hydrogen bonds · protein-protein
- 2–6 · 3483 Ų buried · 28 hydrogen bonds · protein-protein
- 4–6 · 3419 Ų buried · 20 hydrogen bonds · protein-protein
- 4–7 · 3386 Ų buried · 21 hydrogen bonds · protein-protein
- 3–5 · 3359 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- O75717 · AlphaFold monomer V2.0 prediction for wd repeat and hmg-box DNA- binding protein 1… · a predicted model of the same protein · chain F against A, TM-score 1.00
- O75419 · AlphaFold monomer V2.0 prediction for cell division control protein 45 homolog (O75419) · a predicted model of the same protein · chain E against A, TM-score 0.97
- Q9Y248 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein PSF2 (Q9Y248) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9BRT9 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein SLD5 (Q9BRT9) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P33991 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM4 (P33991) · a predicted model of the same protein · chain 4 against A, TM-score 0.94
- Q9BRX5 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein PSF3 (Q9BRX5) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P33993 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM7 (P33993) · a predicted model of the same protein · chain 7 against A, TM-score 0.91
- Q14691 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein PSF1 (Q14691) · a predicted model of the same protein · chain A against A, TM-score 0.91
- P49736 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM2 (P49736) · a predicted model of the same protein · chain 2 against A, TM-score 0.84
- Q14566 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM6 (Q14566) · a predicted model of the same protein · chain 6 against A, TM-score 0.81
- P25205 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM3 (P25205) · a predicted model of the same protein · chain 3 against A, TM-score 0.78
- P33992 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM5 (P33992) · a predicted model of the same protein · chain 5 against A, TM-score 0.68
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
- Every structure of UniProt O75717
- Elsewhere: RCSB PDB 6XTY · PDBe 6XTY · UniProt P49736 · UniProt P25205 · UniProt P33991 · UniProt P33992 · UniProt Q14566 · UniProt P33993 · UniProt Q14691 · UniProt Q9Y248 · UniProt Q9BRX5 · UniProt Q9BRT9 · UniProt O75419 · UniProt O75717
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