8TNR
Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A | DNA damage-binding protein 1 | polymer | 860 | 96033.9 | 1 | UniProt (Q16531) Pfam (PF10433) Pfam (PF03178) In PDB | Homo sapiens (human) | DDB p127 subunit,DNA damage-binding protein a,DDBa,Damage-specific DNA-binding protein 1,HBV X-associated protein 1,XAP-1,UV-damaged DNA-binding factor,UV-damaged DNA-binding protein 1,UV-DDB 1,XPE-binding factor,XPE-BF,Xeroderma pigmentosum group E-complementing protein,XPCe |
2 | B | Protein cereblon | polymer | 485 | 55144.6 | 1 | UniProt (Q96SW2) Pfam (PF02190) Pfam (PF03226) In PDB | Homo sapiens (human) | |
3 | C | Maltose/maltodextrin-binding periplasmic protein,SD40 | polymer | 455 | 50466.0 | 1 | UniProt (P0AEX9) UniProt (Q13422) Pfam (PF01547) Pfam (PF00096) In PDB | Escherichia coli | |
4 | B, C | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
5 | B | 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione | non-polymer | 343.3 | 1 | Chemie (MIQ) |
Sequence modifications
A: 1 - 699 (UniProt: Q16531)
A: 706 - 1140 (UniProt: Q16531)
B: 1 - 442 (UniProt: Q96SW2)
C: -376 - -7 (UniProt: P0AEX9)
C: 15 - 50 (UniProt: Q13422)
PDB | External Database | Details |
---|---|---|
Met -23 | - | initiating methionine |
Gly -22 | - | expression tag |
Ser -21 | - | expression tag |
Ser -20 | - | expression tag |
His -19 | - | expression tag |
His -18 | - | expression tag |
His -17 | - | expression tag |
His -16 | - | expression tag |
His -15 | - | expression tag |
His -14 | - | expression tag |
Ser -13 | - | expression tag |
Ala -12 | - | expression tag |
Val -11 | - | expression tag |
Asp -10 | - | expression tag |
Glu -9 | - | expression tag |
Asn -8 | - | expression tag |
Leu -7 | - | expression tag |
Tyr -6 | - | expression tag |
Phe -5 | - | expression tag |
Gln -4 | - | expression tag |
Gly -3 | - | expression tag |
Gly -2 | - | expression tag |
Gly -1 | - | expression tag |
Arg 0 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Gly 700 | - | linker |
Asn 701 | - | linker |
Gly 702 | - | linker |
Asn 703 | - | linker |
Ser 704 | - | linker |
Gly 705 | - | linker |
PDB | External Database | Details |
---|---|---|
Met -42 | - | initiating methionine |
Asp -41 | - | expression tag |
Tyr -40 | - | expression tag |
Lys -39 | - | expression tag |
Asp -38 | - | expression tag |
Asp -37 | - | expression tag |
Asp -36 | - | expression tag |
Asp -35 | - | expression tag |
Lys -34 | - | expression tag |
Ser -33 | - | expression tag |
Ala -32 | - | expression tag |
Val -31 | - | expression tag |
Asp -30 | - | expression tag |
Glu -29 | - | expression tag |
Asn -28 | - | expression tag |
Leu -27 | - | expression tag |
Tyr -26 | - | expression tag |
Phe -25 | - | expression tag |
Gln -24 | - | expression tag |
Gly -23 | - | expression tag |
Gly -22 | - | expression tag |
Gly -21 | - | expression tag |
Arg -20 | - | expression tag |
Gly -19 | - | expression tag |
Gly -18 | - | expression tag |
Ser -17 | - | expression tag |
Ala -16 | - | expression tag |
His -15 | - | expression tag |
Ile -14 | - | expression tag |
Val -13 | - | expression tag |
Met -12 | - | expression tag |
Val -11 | - | expression tag |
Asp -10 | - | expression tag |
Ala -9 | - | expression tag |
Tyr -8 | - | expression tag |
Lys -7 | - | expression tag |
Pro -6 | - | expression tag |
Thr -5 | - | expression tag |
Lys -4 | - | expression tag |
Gly -3 | - | expression tag |
Gly -2 | - | expression tag |
Ser -1 | - | expression tag |
Gly 0 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Met -404 | - | initiating methionine |
Gly -403 | - | expression tag |
Leu -402 | - | expression tag |
Asn -401 | - | expression tag |
Asp -400 | - | expression tag |
Ile -399 | - | expression tag |
Phe -398 | - | expression tag |
Glu -397 | - | expression tag |
Ala -396 | - | expression tag |
Gln -395 | - | expression tag |
Lys -394 | - | expression tag |
Ile -393 | - | expression tag |
Glu -392 | - | expression tag |
Trp -391 | - | expression tag |
His -390 | - | expression tag |
Glu -389 | - | expression tag |
Gly -388 | - | expression tag |
Ser -387 | - | expression tag |
Ser -386 | - | expression tag |
His -385 | - | expression tag |
His -384 | - | expression tag |
His -383 | - | expression tag |
His -382 | - | expression tag |
His -381 | - | expression tag |
His -380 | - | expression tag |
Gly -379 | - | expression tag |
Ser -378 | - | expression tag |
Ser -377 | - | expression tag |
Leu -6 | - | linker |
Glu -5 | - | linker |
Val -4 | - | linker |
Leu -3 | - | linker |
Phe -2 | - | linker |
Gln -1 | - | linker |
Gly 0 | - | linker |
Pro 1 | - | linker |
Asp 2 | - | linker |
Tyr 3 | - | linker |
Lys 4 | - | linker |
Asp 5 | - | linker |
Asp 6 | - | linker |
Asp 7 | - | linker |
Asp 8 | - | linker |
Lys 9 | - | linker |
Ser 10 | - | linker |
Gly 11 | - | linker |
Gly 12 | - | linker |
Gly 13 | - | linker |
Gly 14 | - | linker |
PDB | External Database | Details |
---|---|---|
Leu 15 | Arg 143 | engineered mutation |
Leu 16 | Pro 144 | engineered mutation |
Leu 17 | Phe 145 | engineered mutation |
Phe 18 | Gln 146 | engineered mutation |
Pro 20 | Asn 148 | engineered mutation |
Ile 21 | Gln 149 | engineered mutation |
Phe 24 | Ala 152 | engineered mutation |
Thr 25 | Ser 153 | engineered mutation |
Cys 26 | Phe 154 | engineered mutation |
Arg 27 | Thr 155 | engineered mutation |
Asn 37 | Lys 165 | engineered mutation |
Thr 40 | Ser 168 | engineered mutation |
Leu 44 | Pro 172 | engineered mutation |
Tyr 47 | Cys 175 | engineered mutation |
Tyr 50 | Cys 178 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 3 |
Total formula weight | 201644.6 | |
Non-Polymers* | Number of molecules | 3 |
Total formula weight | 474.2 | |
All* | Total formula weight | 202118.7 |