MolNFT v1 · #78035 · protein

Crystal structure of the human XRCC4-xlf complex

3RWR · DNA repair protein XRCC4: “Crystal structure of the human XRCC4-xlf complex”. X-ray diffraction, 1 ligand (TBR), 20 pockets (best druggability 0.81). MolNFT v1 #78035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3RWR
Type: protein
Length: 4,581 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein XRCC4; Non-homologous end-joining factor 1
UniProt: Q13426, Q9H9Q4
Ligands: TBR
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein XRCC4	protein	147	24% helix, 20% strand	Q13426
B	DNA repair protein XRCC4	protein	152	25% helix, 24% strand	Q13426
D, E, H, I, L, M, O, Q, W, X	Non-homologous end-joining factor 1	protein	227	43% helix, 15% strand	Q9H9Q4
F, G, J, K, N, P, R, V, U, Y	DNA repair protein XRCC4	protein	157	33% helix, 18% strand	Q13426
S	Non-homologous end-joining factor 1	protein	218	42% helix, 16% strand	Q9H9Q4
T	Non-homologous end-joining factor 1	protein	224	43% helix, 15% strand	Q9H9Q4

Ligands and binding sites

TBR · Hexatantalum dodecabromide · ligand · 8 copies · chains D, H, J, M, P, V, X, U, Y

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	144	0.81	0.97	36	empty
2	1111	0.78	0.79	100	empty
3	143	0.77	0.94	30	empty
4	176	0.76	0.92	30	empty
5	990	0.75	0.77	82	empty

Interfaces

33 interfaces between chains.

O–Q · 3499 Å² buried · 27 hydrogen bonds · protein-protein
S–W · 3487 Å² buried · 28 hydrogen bonds · protein-protein
H–I · 3464 Å² buried · 27 hydrogen bonds · protein-protein
T–X · 3417 Å² buried · 23 hydrogen bonds · protein-protein
L–M · 3397 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3RWR · Crystal structure of the human XRCC4-XLF complex · the same entry in another collection · chain L against L, 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 Q13426
Every structure of UniProt Q9H9Q4
Elsewhere: RCSB PDB 3RWR · PDBe 3RWR · UniProt Q13426 · UniProt Q9H9Q4

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