MolNFT v1 · #86432 · protein

Structure of HDCP1A in complex with proline rich sequence of PNRC2

4B6H · MRNA-decapping enzyme 1A: “Structure of HDCP1A in complex with proline rich sequence of PNRC2”. X-ray diffraction, 2 pockets (best druggability 0.37). MolNFT v1 #86432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4B6H
Type: protein
Length: 256 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA-decapping enzyme 1A; Proline-rich nuclear receptor coactivator 2
EC: 3.-.-.-
UniProt: Q9NPI6, Q9NPJ4
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA-decapping enzyme 1A (EC 3.-.-.-)	protein	129	26% helix, 47% strand	Q9NPI6
B	MRNA-decapping enzyme 1A (EC 3.-.-.-)	protein	100	13% helix, 54% strand	Q9NPI6
C	Proline-rich nuclear receptor coactivator 2	protein	14	21% helix, 0% strand	Q9NPJ4
D	Proline-rich nuclear receptor coactivator 2	protein	13	23% helix, 0% strand	Q9NPJ4

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	106	0.37	0.75	23	empty
2	68	0.35	0.76	19	empty

Interfaces

3 interfaces between chains.

A–C · 733 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 669 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 361 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4B6H · Structure of hDcp1a in complex with proline rich sequence of PNRC2 · the same entry in another collection · chain D against D, TM-score 1.00
Q9NPI6 · AlphaFold monomer V2.0 prediction for mRNA-decapping enzyme 1A (Q9NPI6) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q9NPJ4 · AlphaFold monomer V2.0 prediction for proline-rich nuclear receptor coactivator 2 (Q9NPJ4) · a predicted model of the same protein · chain D against A, TM-score 0.47

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 Q9NPI6
Every structure of UniProt Q9NPJ4
Elsewhere: RCSB PDB 4B6H · PDBe 4B6H · UniProt Q9NPI6 · UniProt Q9NPJ4

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