6GJW: XIAP-BIR1 domain

Structure of XIAP-BIR1 domain in complex with an NF023 analog. Determined by X-ray diffraction at 1.9 Å resolution. Released 29 May 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,759
Mol. weight: 51.43 kDa
Ligands: ZN, F2H
Released: 29 May 2019

Explore 6GJW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GJW contains 17 α-helices and 12 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
α-helix	26-30	5
α-helix	31-33	3
α-helix	44-49	6
β-strand	52-54	3	1
β-strand	61-63	3	1
β-strand	69-70	2	1
α-helix	79-86	8

Chains B and D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
α-helix	26-31	6
α-helix	44-49	6
β-strand	52-54	3	2
β-strand	61-63	3	2
β-strand	69-70	2	2
α-helix	79-86	8

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-30	5
α-helix	31-33	3
α-helix	44-49	6
β-strand	52-54	3	3
β-strand	61-63	3	3
β-strand	69-70	2	3
α-helix	79-86	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase XIAP	A, B, C, D	protein	111	Homo sapiens	P98170 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6GJW_1 E3 ubiquitin-protein ligase XIAP (chains A, B, C, D)
MGSSHHHHHHSSGLVPQGSHMKTCVPADINKEEEFVEEFNRLKTFANFPSGSPVSASTLA
RAGFLYTGEGDTVRCFSCHAAVDRWQYGDSAVGRHRKVSPNCRFINGFYLE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
F2H	4-[[3-[[3-[(4,8-disulfonatonaphthalen-1-yl)carbamoyl]phenyl]carbamoylamino]phen…	C35 H22 N4 O15 S4	2

Primary citation

Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1. Sorrentino, L., Cossu, F., Milani, M. et al. ChemistryOpen (2019) 8:476-482. DOI 10.1002/open.201900059 · PubMed

Other PDB entries of the same protein (UniProt P98170 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4J44 1.3 Å, Crystal structure of XIAP-BIR2 domain with AIAV bound
8W59 1.34 Å, Crystal structure of the RING domain of human XIAP treated with arsenic trioxide
4J47 1.35 Å, Crystal structure of XIAP-BIR2 domain with SVPI bound
4J46 1.42 Å, Crystal structure of XIAP-BIR2 domain with AVPI bound
4J3Y 1.45 Å, Crystal structure of XIAP-BIR2 domain
4J45 1.48 Å, Crystal structure of XIAP-BIR2 domain with ATAA bound
5O6T 1.57 Å, BIRC4 RING in complex with dimeric ubiquitin variant
4KJU 1.6 Å, Crystal structure of XIAP-Bir2 with a bound benzodiazepinone inhibitor.
8W5A 1.65 Å, Crystal structure of the RING domain of human XIAP
4KJV 1.7 Å, Crystal structure of XIAP-Bir2 with a bound spirocyclic benzoxazepinone inhibitor.
3UW5 1.71 Å, Crystal structure of the BIR domain of MLIAP bound to GDC0152
8GH7 1.75 Å, 142D6 bound to BIR3-XIAP

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