Experimental coordinates · Exact deposited instances

Ligand contacts & pocket quality

Inspect the atoms that are present, the residues that are missing, and the precise scope of each chemical association.

DNMT3B PWWP18EII · chain BPWWP_POCKET_QUALITY_1.0.0

PDB entry Protein label chain PWWP domain Deposited ligand instance

Phase 6C historical atom / receptor assessment Phase 6C.1 full-atom experimental quality inventory

Full-coordinate Phase 6C.1 atom and ligand environment assessment

ExamplesNSD2 · UNC6934 NSD3 · BI-9321 11OA · missing side chains

8EIIInspect the deposited atoms

Load the checksum-verified original coordinates to explore the selected chain and ligand.

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Atom completeness · selected chain and annotation core

What can these coordinates support?

Export selected evidence

Select a source-recorded contacting residue to inspect its deposited numbering.

A fully observed annotation core is not a complete-receptor certification. Short annotation intervals, absent peripheral residues, alternate conformers and unexamined density can limit structural interpretation. No receptor preparation was performed.

Frozen 5 Å heavy-atom proximity observations

Contacting residues · SAH

19 full-chain residues

Heavy-atom distances use the first deposited model and asymmetric unit, occupancy >0 and retained alternate locations. No symmetry expansion or affinity inference. Proximity alone is not evidence of affinity or a functional interaction.

Canonical residue	Deposited residue	Scope	Minimum distance	Atom quality
PHE 581	B:581 · entity 378 · label B	outside PWWP annotations	3.2550 Å	Unassessed
ASP 582	B:582 · entity 379 · label B	outside PWWP annotations	3.4486 Å	Unassessed
GLY 583	B:583 · entity 380 · label B	outside PWWP annotations	3.8165 Å	Unassessed
ILE 584	B:584 · entity 381 · label B	outside PWWP annotations	4.2955 Å	Unassessed
THR 586	B:586 · entity 383 · label B	outside PWWP annotations	3.5627 Å	Unassessed
SER 604	B:604 · entity 401 · label B	outside PWWP annotations	3.7025 Å	Unassessed
GLU 605	B:605 · entity 402 · label B	outside PWWP annotations	2.2050 Å	Unassessed
VAL 606	B:606 · entity 403 · label B	outside PWWP annotations	3.8910 Å	Unassessed
CYS 607	B:607 · entity 404 · label B	outside PWWP annotations	3.7069 Å	Unassessed
ASP 627	B:627 · entity 424 · label B	outside PWWP annotations	2.9064 Å	Unassessed
VAL 628	B:628 · entity 425 · label B	outside PWWP annotations	3.4894 Å	Unassessed
ARG 629	B:629 · entity 426 · label B	outside PWWP annotations	4.6008 Å	Unassessed
GLY 648	B:648 · entity 445 · label B	outside PWWP annotations	4.2166 Å	Unassessed
PRO 650	B:650 · entity 447 · label B	outside PWWP annotations	4.2995 Å	Unassessed
LEU 671	B:671 · entity 468 · label B	outside PWWP annotations	4.6308 Å	Unassessed
GLU 697	B:697 · entity 494 · label B	outside PWWP annotations	4.8156 Å	Unassessed
ARG 832	B:832 · entity 629 · label B	outside PWWP annotations	3.5347 Å	Unassessed
SER 833	B:833 · entity 630 · label B	outside PWWP annotations	3.3042 Å	Unassessed
TRP 834	B:834 · entity 631 · label B	outside PWWP annotations	3.3506 Å	Unassessed

Identity, native target and exact site links

Linked experimental assays

Measured preparation	Method / endpoint	Original observation	Tested construct	Evidence
No exact site-to-assay link is established in the frozen evidence graph. Visit the domain's Ligands & Bioactivity section for newly curated or structure-free observations.

Filterable structural assessment inventory

Coordinate coverage & quality

666 chain/domain records · 22 assessed for atom completeness

86 selected chain/domain records. Ligand counts mean deposited proximity; all-atom completeness is assessed only where specified.
PDB / chain	Domain	Core Cα coverage	PWWP-contact ligand instances	Atom assessment	Missing core heavy atoms
3FLG · A	DNMT3B PWWP1	59 / 59	0	Unassessed	—
3QKJ · A	DNMT3B PWWP1	59 / 59	4	Unassessed	—
3QKJ · B	DNMT3B PWWP1	59 / 59	3	Unassessed	—
3QKJ · C	DNMT3B PWWP1	59 / 59	1	Unassessed	—
3QKJ · D	DNMT3B PWWP1	59 / 59	5	Unassessed	—
5CIU · A	DNMT3B PWWP1	59 / 59	1	Unassessed	—
5CIU · B	DNMT3B PWWP1	59 / 59	2	Unassessed	—
5NR3 · A	DNMT3B PWWP1	59 / 59	4	Unassessed	—
5NR3 · B	DNMT3B PWWP1	59 / 59	2	Unassessed	—
5NRR · A	DNMT3B PWWP1	59 / 59	5	Unassessed	—
5NRR · B	DNMT3B PWWP1	59 / 59	4	Unassessed	—
5NRS · A	DNMT3B PWWP1	59 / 59	4	Unassessed	—
5NRS · B	DNMT3B PWWP1	59 / 59	5	Unassessed	—
5NRV · A	DNMT3B PWWP1	59 / 59	7	Unassessed	—
5NRV · B	DNMT3B PWWP1	59 / 59	7	Unassessed	—
5NV0 · A	DNMT3B PWWP1	59 / 59	7	Unassessed	—
5NV0 · B	DNMT3B PWWP1	59 / 59	8	Unassessed	—
5NV2 · A	DNMT3B PWWP1	59 / 59	7	Unassessed	—
5NV2 · B	DNMT3B PWWP1	59 / 59	6	Unassessed	—
5NV7 · A	DNMT3B PWWP1	59 / 59	4	Unassessed	—
5NV7 · B	DNMT3B PWWP1	59 / 59	5	Unassessed	—
5NVO · A	DNMT3B PWWP1	59 / 59	8	Unassessed	—
5NVO · B	DNMT3B PWWP1	59 / 59	7	Unassessed	—
6PA7 · L	DNMT3B PWWP1	0 / 59	0	Unassessed	—
6PA7 · N	DNMT3B PWWP1	0 / 59	0	Unassessed	—
6R3E · A	DNMT3B PWWP1	59 / 59	4	Unassessed	—
6R3E · B	DNMT3B PWWP1	59 / 59	1	Unassessed	—
8EIH · A	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIH · B	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIH · C	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIH · D	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIH · E	DNMT3B PWWP1	59 / 59	0	Unassessed	—
8EII · A	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EII · B	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EII · C	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EII · D	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIJ · A	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIJ · B	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIJ · C	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIK · A	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIK · B	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIK · C	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIK · D	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIK · E	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8EIK · F	DNMT3B PWWP1	0 / 59	0	Unassessed	—
8ZLK · A	DNMT3B PWWP1	59 / 59	0	Unassessed	—
8ZLK · B	DNMT3B PWWP1	59 / 59	0	Unassessed	—
9E00 · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E00 · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E00 · W	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E00 · X	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E05 · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E05 · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E05 · W	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E05 · X	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E0F · A	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E0F · B	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E0G · A	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E0G · B	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2D · Q	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2D · R	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2D · U	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2D · V	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2Q · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2Q · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2Q · W	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2Q · X	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2R · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2R · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2R · W	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E2R · X	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3D · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3D · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3R · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3R · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3R · W	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3R · X	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3U · I	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3U · L	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9E3U · M	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9Q7U · K	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9Q7U · L	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9Y4P · S	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9Y4P · T	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9Y4P · W	DNMT3B PWWP1	0 / 59	0	Unassessed	—
9Y4P · X	DNMT3B PWWP1	0 / 59	0	Unassessed	—

Source bytes, methods and provenance

Detailed atom completeness only for the three packaged original-coordinate files; quality uses observed atom-name union across positive-occupancy alternate conformers, with per-alt differences retained. Missing entire residues are separate. Nonstandard amino-acid templates are unassessed. No density reinterpretation, receptor repair, docking or MD.

Coordinate SHA-256: 5035b50d97c6361eeec23854535f33b7f8dfc997bdf34bb2665fededdf1c19bd

Source PDB: https://www.rcsb.org/structure/8EII. Original coordinate file: mmCIF. Original annotation and contact calculations are retained unchanged; the additional completeness assessment is PWWP_POCKET_QUALITY_1.0.0.

Methods and reproducible builder are included under analysis/phase5_pockets and scripts/build_phase5_pockets.py in the downloadable release.

8EII · SAH

What can these coordinates support?

Contacting residues · SAH

Linked experimental assays

Coordinate coverage & quality