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.

DNMT3A PWWP111OA · chain DPWWP_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

11OAInspect 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

Core residues observed0 / 59

Unobserved core residues59

Missing heavy atoms in observed core0

Missing backbone atoms in observed core0

Standard atoms presentMissing heavy atomsUnobserved residueTemplate unassessed

Select a residue to inspect atom names, deposited numbering, alternate conformers and coordinate gaps.

Construct substitutions, alternate conformers and interpretation

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.

Source-recorded construct sequence mismatches: [{"construct": "H", "entity_position": 603, "reference": "R", "uniprot_position": 882}]. Observed core substitutions: [].

Core residues with alternate conformers: 0. Alternate-specific completeness is retained in the selected JSON export. Missing coordinates have not been filled.

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 · ZN

8 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
CYS 549	D:549 · entity 270 · label D	outside PWWP annotations	2.3337 Å	Standard atoms present
ASN 551	D:551 · entity 272 · label D	outside PWWP annotations	4.0938 Å	Standard atoms present
CYS 554	D:554 · entity 275 · label D	outside PWWP annotations	2.3322 Å	Standard atoms present
CYS 555	D:555 · entity 276 · label D	outside PWWP annotations	4.8799 Å	Standard atoms present
ARG 556	D:556 · entity 277 · label D	outside PWWP annotations	3.9112 Å	Standard atoms present
ASN 582	D:582 · entity 303 · label D	outside PWWP annotations	4.9463 Å	Standard atoms present
CYS 583	D:583 · entity 304 · label D	outside PWWP annotations	2.3260 Å	Standard atoms present
CYS 586	D:586 · entity 307 · label D	outside PWWP annotations	2.3133 Å	Standard atoms present

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

104 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
11NZ · A	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11NZ · B	DNMT3A PWWP1	59 / 59	0	Unassessed	—
11NZ · C	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11NZ · D	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11NZ · E	DNMT3A PWWP1	59 / 59	0	Unassessed	—
11NZ · F	DNMT3A PWWP1	59 / 59	0	Unassessed	—
11NZ · G	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11NZ · H	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11NZ · I	DNMT3A PWWP1	59 / 59	0	Unassessed	—
11NZ · J	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OA · A	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · B	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · C	DNMT3A PWWP1	59 / 59	0	Assessed	198
11OA · D	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · E	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · F	DNMT3A PWWP1	59 / 59	0	Assessed	198
11OA · G	DNMT3A PWWP1	59 / 59	0	Assessed	198
11OA · H	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · I	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · J	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · K	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · L	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · M	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · N	DNMT3A PWWP1	59 / 59	0	Assessed	198
11OA · O	DNMT3A PWWP1	59 / 59	0	Assessed	198
11OA · P	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · Q	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OA · R	DNMT3A PWWP1	0 / 59	0	Assessed	0
11OH · A	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OH · B	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OH · C	DNMT3A PWWP1	59 / 59	0	Unassessed	—
11OH · D	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OI · A	DNMT3A PWWP1	59 / 59	0	Unassessed	—
11OI · B	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OI · C	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OI · D	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OI · E	DNMT3A PWWP1	0 / 59	0	Unassessed	—
11OI · F	DNMT3A PWWP1	59 / 59	0	Unassessed	—
3LLR · A	DNMT3A PWWP1	59 / 59	1	Unassessed	—
3LLR · B	DNMT3A PWWP1	59 / 59	2	Unassessed	—
3LLR · C	DNMT3A PWWP1	59 / 59	1	Unassessed	—
3LLR · D	DNMT3A PWWP1	59 / 59	1	Unassessed	—
3LLR · E	DNMT3A PWWP1	59 / 59	1	Unassessed	—
6PA7 · K	DNMT3A PWWP1	0 / 59	0	Unassessed	—
6PA7 · M	DNMT3A PWWP1	0 / 59	0	Unassessed	—
8QZM · K	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E00 · U	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E00 · V	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E00 · Y	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E00 · Z	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E05 · U	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E05 · V	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E05 · Y	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E05 · Z	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E0F · C	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E0F · D	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E0G · C	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E0G · D	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E2D · S	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2D · T	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E2D · W	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2D · X	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E2Q · U	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2Q · V	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2Q · Y	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2Q · Z	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2R · U	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2R · V	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E2R · Y	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E2R · Z	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E3D · U	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E3D · V	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9E3R · U	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E3R · V	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E3R · Y	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E3R · Z	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E3U · N	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9E3U · O	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9LQ1 · A	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9LQ1 · D	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · A	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · B	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · C	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · D	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · E	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · F	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · G	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MP0 · H	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPO · A	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPO · B	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPO · C	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPO · D	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPO · E	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPO · F	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPP · K	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9MPP · M	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9PRW · A	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9PRW · D	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9Q7U · M	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9Q7U · N	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9Y4P · U	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9Y4P · V	DNMT3A PWWP1	59 / 59	0	Unassessed	—
9Y4P · Y	DNMT3A PWWP1	0 / 59	0	Unassessed	—
9Y4P · Z	DNMT3A PWWP1	0 / 59	0	Unassessed	—

Source bytes, methods and provenance

Coordinate SHA-256: 22b69191b56482b52a2cc8a8a6f517b143b90300e647239a8ef53c45b3c5873c

Source PDB: https://www.rcsb.org/structure/11OA. 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.

11OA · ZN

What can these coordinates support?

Contacting residues · ZN

Linked experimental assays

Coordinate coverage & quality