Research workbench
Structure of inner kinetochore ccan-cenp-a complex
Analyse Structure of inner kinetochore ccan-cenp-a complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QLD
- Type
- protein + DNA
- Length
- 3,405 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner kinetochore subunit MIF2; DNA (125-mer); Inner kinetochore subunit MCM16; Inner…
- UniProt
- P35201, Q12262, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162, P36012, P02309, P02294, P04911, P02293
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 21 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Inner kinetochore subunit MIF2 | protein | 22 | 0% helix, 0% strand | P35201 |
| G | DNA (125-mer) | dna | 124 | — | — |
| H | Inner kinetochore subunit MCM16 | protein | 125 | 84% helix, 0% strand | Q12262 |
| I | Inner kinetochore subunit CTF3 | protein | 362 | 59% helix, 0% strand | Q12748 |
| J | DNA (125-mer) | dna | 124 | — | — |
| K | Inner kinetochore subunit MCM22 | protein | 106 | 89% helix, 0% strand | P47167 |
| L | Inner kinetochore subunit IML3 | protein | 241 | 27% helix, 21% strand | P38265 |
| N | Inner kinetochore subunit CHL4 | protein | 371 | 35% helix, 17% strand | P38907 |
| O | Inner kinetochore subunit MCM21 | protein | 205 | 37% helix, 24% strand | Q06675 |
| P | Inner kinetochore subunit CTF19 | protein | 242 | 37% helix, 29% strand | Q02732 |
| Q | Inner kinetochore subunit OKP1 | protein | 204 | 73% helix, 1% strand | P53298 |
| U | Inner kinetochore subunit AME1 | protein | 171 | 81% helix, 0% strand | P38313 |
| Y | Inner kinetochore subunit NKP1 | protein | 223 | 74% helix, 0% strand | Q12493 |
| Z | Inner kinetochore subunit NKP2 | protein | 140 | 79% helix, 0% strand | Q06162 |
| a | Histone H3-like centromeric protein CSE4 | protein | 87 | 64% helix, 1% strand | P36012 |
| b, f | Histone H4 | protein | 79 | 62% helix, 5% strand | P02309 |
| d | Histone H2B.2 | protein | 93 | 75% helix, 4% strand | P02294 |
| e | Histone H3-like centromeric protein CSE4 | protein | 106 | 66% helix, 3% strand | P36012 |
| g | Histone H2A.1 | protein | 105 | 50% helix, 3% strand | P04911 |
| h | Histone H2B.1 | protein | 94 | 72% helix, 0% strand | P02293 |
| i | Histone H2A.1 | protein | 102 | 49% helix, 4% strand | P04911 |
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 | 1019 | 0.85 | 0.86 | 124 | empty |
| 2 | 862 | 0.83 | 0.84 | 79 | empty |
| 3 | 1130 | 0.81 | 0.82 | 109 | empty |
| 4 | 926 | 0.79 | 0.81 | 78 | empty |
| 5 | 800 | 0.78 | 0.82 | 73 | empty |
Interfaces
70 interfaces between chains.
- G–J · 5725 Ų buried · 461 hydrogen bonds · nucleic-nucleic
- Y–Z · 3304 Ų buried · 9 hydrogen bonds · protein-protein
- Q–U · 2880 Ų buried · 10 hydrogen bonds · protein-protein
- H–K · 2778 Ų buried · 9 hydrogen bonds · protein-protein
- g–h · 2619 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6QLD · Structure of inner kinetochore CCAN-Cenp-A complex · the same entry in another collection · chain K against K, 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 P35201
- Every structure of UniProt Q12262
- Every structure of UniProt Q12748
- Every structure of UniProt P47167
- Every structure of UniProt P38265
- Every structure of UniProt P38907
- Every structure of UniProt Q06675
- Every structure of UniProt Q02732
- Every structure of UniProt P53298
- Every structure of UniProt P38313
- Every structure of UniProt Q12493
- Every structure of UniProt Q06162
- Every structure of UniProt P36012
- Every structure of UniProt P02309
- Every structure of UniProt P02294
- Every structure of UniProt P04911
- Every structure of UniProt P02293
- Elsewhere: RCSB PDB 6QLD · PDBe 6QLD · UniProt P35201 · UniProt Q12262 · UniProt Q12748 · UniProt P47167 · UniProt P38265 · UniProt P38907 · UniProt Q06675 · UniProt Q02732 · UniProt P53298 · UniProt P38313 · UniProt Q12493 · UniProt Q06162 · UniProt P36012 · UniProt P02309 · UniProt P02294 · UniProt P04911 · UniProt P02293
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