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Structure paper

TitleOrf9b homodimer in complex with fragments
Journal, issue, pagesto be published
Publish dateOct 19, 2025 (structure data deposition date)
AuthorsSan Felipe, C.J. / Fraser, J.S.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.37 - 2.39 Å
Structure data

PDB-13tc:
Orf9b homodimer in complex with fragment ZINC000039281982
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-13td:
Orf9b homodimer in complex with fragment ZINC000008614810
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-13te:
Orf9b homodimer in complex with fragment ZINC000000164607
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-13tf:
Orf9b homodimer in complex with fragment ZINC000000158741
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-13tg:
Orf9b homodimer in complex with fragment ZINC000000152502
Method: X-RAY DIFFRACTION / Resolution: 2.39 Å

PDB-13th:
Orf9b homodimer in complex with fragment ZINC000018154848
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-13ti:
Orf9b homodimer in complex with fragment ZINC000002560357
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-13tj:
Orf9b homodimer in complex with fragment ZINC000000158540
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-13tk:
Orf9b homodimer in complex with fragment ZINC000000174344
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-13tl:
Orf9b homodimer in complex with fragment ZINC000020213524
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-13tm:
Orf9b homodimer in complex with fragment ZINC000020283605
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-13tn:
Orf9b homodimer in complex with fragment ZINC000000388280
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-13to:
Orf9b homodimer in complex with fragment ZINC000084843283
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-13tp:
Orf9b homodimer in complex with fragment ZINC000000156863
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-13tq:
Orf9b homodimer in complex with fragment ZINC000006657973
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-13tr:
Orf9b homodimer in complex with fragment ZINC000004219237
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-13ts:
Orf9b homodimer in complex with fragment ZINC000000164504
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-13tt:
Orf9b homodimer in complex with fragment ZINC000019015078
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-13tu:
Orf9b homodimer in complex with fragment ZINC000037716618
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-13tv:
Orf9b homodimer in complex with fragment ZINC000000146551
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-13tw:
Orf9b homodimer in complex with fragment ZINC000000002055
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-13tx:
Orf9b homodimer in complex with fragment ZINC000000107891
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-13ty:
Orf9b homodimer in complex with fragment ZINC000000337835
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-13tz:
Orf9b homodimer in complex with fragment ZINC000000083028
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-13ua:
Orf9b homodimer in complex with fragment ZINC000002508153
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-13ub:
Orf9b homodimer in complex with fragment ZINC000000053963
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-13uc:
Orf9b homodimer in complex with fragment ZINC000038866729
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-13ud:
Orf9b homodimer in complex with fragment ZINC000000404753
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-13ue:
Orf9b homodimer in complex with fragment ZINC000000459533
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-13uf:
Orf9b homodimer in complex with fragment ZINC000000158156
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-13ug:
Orf9b homodimer in complex with fragment ZINC000004787230
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-13uh:
Orf9b homodimer in complex with fragment ZINC000004218283
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-13ui:
Orf9b homodimer in complex with fragment ZINC000008615114
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-13uj:
Orf9b homodimer in complex with fragment ZINC000006661362
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-13uk:
Orf9b homodimer in complex with fragment ZINC000000120508
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-13ul:
Orf9b homodimer in complex with fragment ZINC000000123600
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-13um:
Orf9b homodimer in complex with fragment ZINC000001389101
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-13un:
Orf9b homodimer in complex with fragment ZINC000002582714
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-13uo:
Orf9b homodimer in complex with fragment ZINC000008981465
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-13up:
Orf9b homodimer in complex with fragment ZINC000001729552
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-13uq:
Orf9b homodimer in complex with fragment ZINC000001689349
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-13ur:
Orf9b homodimer in complex with fragment ZINC000000394620
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-13us:
Orf9b homodimer in complex with fragment ZINC000001683100
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-13ut:
Orf9b homodimer in complex with fragment ZINC000016697555
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-13uu:
Orf9b homodimer in complex with fragment ZINC000020269204
Method: X-RAY DIFFRACTION / Resolution: 2.07 Å

PDB-13uv:
Orf9b homodimer in complex with fragment ZINC000017744334
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-13uw:
Orf9b homodimer in complex with fragment ZINC000002386971
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-13ux:
Orf9b homodimer in complex with fragment ZINC000034977567
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-13uy:
Orf9b homodimer in complex with Enamine Z992449454
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-13uz:
Orf9b homodimer in complex with Enamine Z1682226079
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-13va:
Orf9b homodimer in complex with Enamine Z3234951291
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

Chemicals

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-D10:
DECANE

ChemComp-2FX:
1-benzothiophen-2-ylacetic acid

ChemComp-HOH:
WATER

ChemComp-36R:
5-chloro-1,3-benzoxazol-2-amine

ChemComp-8P7:
2-methyl-1~{H}-benzimidazole

ChemComp-ICO:
1H-INDOLE-3-CARBOXYLIC ACID

ChemComp-SX1:
2-amino-5-bromobenzoic acid

ChemComp-4HC:
4-HYDROXY-2H-CHROMEN-2-ONE

ChemComp-LSA:
1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE

ChemComp-0HN:
1,3-benzodioxole-5-carboxylic acid

ChemComp-SQ7:
3-(4-chlorophenyl)imidazole-2,4-dione

PDB-1c1g:
CRYSTAL STRUCTURE OF TROPOMYOSIN AT 7 ANGSTROMS RESOLUTION IN THE SPERMINE-INDUCED CRYSTAL FORM

PDB-1c1h:
CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH N-METHYL MESOPORPHYRIN

ChemComp-54G:
2-hydroxy-5-methylbenzoic acid

ChemComp-CLW:
CHLORZOXAZONE

ChemComp-3BZ:
3-chlorobenzoate

ChemComp-5GT:
7-(trifluoromethyl)-3,4-dihydroquinoxalin-2(1H)-one

ChemComp-6U6:
3-(5-chloranyl-1,3-benzothiazol-2-yl)propanoic acid

ChemComp-BZX:
1,3-benzodioxol-5-ol

ChemComp-4JO:
5-bromo-6-methylpyridin-2-amine

PDB-1c1i:
Unknown entry

PDB-1c1j:
STRUCTURE OF CADMIUM-SUBSTITUTED PHOSPHOLIPASE A2 FROM AGKISTRONDON HALYS PALLAS AT 2.8 ANGSTROMS RESOLUTION

ChemComp-OHB:
salicylamide

ChemComp-NUK:
thieno[3,2-b]thiophene-5-carboxylic acid

ChemComp-6FZ:
2,3-dihydro-1H-indene-2-carboxylic acid

ChemComp-FIC:
5-fluoroindole-2-carboxylic acid

ChemComp-4BY:
5-methyl-1H-indole-2-carboxylic acid

ChemComp-BZ2:
1-benzofuran-2-carboxylic acid

ChemComp-5LA:
2-chloranyl-6~{H}-thieno[2,3-b]pyrrole-5-carboxylic acid

ChemComp-BRB:
PARA-BROMOBENZYL ALCOHOL

ChemComp-36Y:
4-(4-bromophenyl)-1H-imidazole

ChemComp-BZ3:
5-methoxy-1H-indole

ChemComp-3R6:
2-hydroxy-5-(methylsulfanyl)benzoic acid

ChemComp-ZZA:
1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID

ChemComp-2D0:
4-chloro-1,3-benzothiazol-2-amine

ChemComp-3AE:
4-(trifluoromethyl)benzoic acid

ChemComp-DBA:
(2,6-DIMETHYL-PHENOXY)-ACETIC ACID

ChemComp-KNL:
(2,6-dichlorophenoxy)acetic acid

ChemComp-4BL:
6-methyl-1H-indole-2-carboxylic acid

ChemComp-2SX:
(5-bromo-1H-indol-3-yl)acetic acid

ChemComp-4ZA:
6H-thieno[2,3-b]pyrrole-5-carboxylic acid

PDB-1c1k:
BACTERIOPHAGE T4 GENE 59 HELICASE ASSEMBLY PROTEIN

PDB-1c1l:
LACTOSE-LIGANDED CONGERIN I

ChemComp-MAJ:
indane-5-sulfonamide

ChemComp-W6A:
4-chloro-1H-indole-2-carboxylic acid

ChemComp-LVF:
2-(5-chloranyl-1H-indol-3-yl)ethanenitrile

PDB-1buq:
SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED WITH THE STEROID 19-NORTESTOSTERONE-HEMISUCCINATE

ChemComp-FBB:
6-fluoro-1,3-benzothiazol-2-amine

PDB-1c1m:
PORCINE ELASTASE UNDER XENON PRESSURE (8 BAR)

PDB-1c1n:
RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

PDB-1c1o:
RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

PDB-1c1p:
RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

PDB-1c1q:
RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Homodimer / SARS-CoV-2 / Innate immunity

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