Structural correspondence

HDGF and NSD3 core comparison

Model A · Blue · Moving

HDGF PWWP1

1RI0:A:UP:P51858:PWWP1 · 58 observed crop residues

Model B · Orange · Fixed

NSD3 PWWP2

4RXJ:A:UP:Q9BZ95:PWWP2 · 63 observed crop residues

Kabsch RMSD2.74983 ÅLeast-squares fit shown below

Aligned Cα atoms56Recorded residue correspondence

TM score · Model A0.66466Normalized by A's 58-residue crop

TM score · Model B0.62562Normalized by B's 63-residue crop

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Reading the local coordinate models and recorded Kabsch transformation…

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Blue: moving model A. Orange: fixed model B. Canonical UniProt numbering is retained.

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How to read this comparison

Download comparison JSON

Only annotation-core Cα atoms are shown. Thin guides connect consecutive canonical positions separated by at most 4.5 Å; they show the fold and are not all-atom covalent bonds. Sequence gaps remain visible.

The blue model uses the recorded Kabsch least-squares fit on US-align residue correspondence. The viewer does not use the separate TM-optimized US-align transformation.

Conservative display criterion (both TM scores ≥0.5 and both aligned fractions ≥0.8): 1. This criterion is a descriptive filter for short cores, not proof of equivalent pockets.

Fit statistics and normalization

US-align reported RMSD: 2.75 Å
Recomputed Kabsch RMSD: 2.74983 Å · transformation displayed above
RMSD under US-align TM transform: 2.992046 Å · separate, undisplayed transformation
Aligned fraction of Model A: 0.965517
Aligned fraction of Model B: 0.888889
Aligned sequence identity: 0.286

The two TM scores each use the corresponding observed crop length as their denominator. The JSON download includes both coordinate models, the applied transformation and all residue correspondences.

Inspect the alignment

Residue correspondence

56 aligned pairs

Canonical UniProt positions in each native domain. The US-align marker describes alignment closeness, not chemical equivalence.

Show all 56 residue correspondences

HDGF position	Residue	NSD3 position	Residue	Alignment marker
12	C	960	Y	:
13	G	961	K	:
14	D	962	Q	:
15	L	963	I	:
16	V	964	V	:
17	F	965	W	:
18	A	966	V	:
19	K	967	K	:
20	M	968	L	:
21	K	969	G	:
22	G	970	N	.
23	Y	971	Y	.
24	P	972	R	:
25	H	973	W	:
26	W	974	W	:
27	P	975	P	:
28	A	976	A	:
29	R	977	E	:
30	I	978	I	:
31	D	979	C	:
32	E	980	N	:
33	M	981	P	:
34	P	982	R	:
35	E	984	V	.
36	A	985	P	.
37	A	986	L	:
38	V	989	Q	:
39	K	990	G	:
40	S	991	L	.
41	T	993	H	.
42	A	995	L	:
43	N	996	G	:
44	K	997	D	:
45	Y	998	F	:
46	Q	999	P	:
47	V	1000	V	:
48	F	1001	F	:
49	F	1002	F	:
50	F	1003	F	:
51	G	1004	G	:
52	T	1005	S	:
53	H	1006	H	:
54	E	1007	D	:
55	T	1008	Y	:
56	A	1009	Y	:
57	F	1010	W	:
58	L	1011	V	:
59	G	1012	H	:
60	P	1013	Q	:
61	K	1014	G	:
62	D	1015	R	:
63	L	1016	V	:
64	F	1017	F	:
65	P	1018	P	:
66	Y	1019	Y	:
67	E	1020	V	.