MolNFT v1 · #162497 · protein + DNA

D. melanogaster cmg-DNA, state 2B

6RAZ: “D. melanogaster cmg-DNA, state 2B”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.89). MolNFT v1 #162497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RAZ
Type: protein + DNA
Length: 4,787 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA; CDC45L; IP07275P; Probable DNA replication complex gins protein PSF2; AT18545P; DNA…
EC: 3.6.4.12
UniProt: O96989, Q9W0I7, Q9VQY9, Q9W2V7, Q9VBI1, P49735, Q9VGW6, Q9V461, Q9XYU1, Q26454, Q9XYU0
Ligands: ATP, ADP
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 13 distinct chains · 30% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	DNA	dna	21	—	—
Y	DNA	dna	2	—	—
A	CDC45L	protein	519	38% helix, 6% strand	O96989
H	IP07275P	protein	195	38% helix, 0% strand	Q9W0I7
L	Probable DNA replication complex gins protein PSF2	protein	179	33% helix, 6% strand	Q9VQY9
M	AT18545P	protein	150	33% helix, 3% strand	Q9W2V7
N	DNA replication complex gins protein SLD5	protein	206	46% helix, 2% strand	Q9VBI1
2	DNA replication licensing factor MCM2 (EC 3.6.4.12)	protein	559	30% helix, 8% strand	P49735
5	DNA replication licensing factor MCM5 (EC 3.6.4.12)	protein	571	24% helix, 7% strand	Q9VGW6
6	DNA replication licensing factor MCM6 (EC 3.6.4.12)	protein	588	28% helix, 6% strand	Q9V461
3	DNA replication licensing factor MCM3 (EC 3.6.4.12)	protein	590	24% helix, 11% strand	Q9XYU1
4	DNA replication licensing factor MCM4 (EC 3.6.4.12)	protein	606	24% helix, 10% strand	Q26454
7	DNA replication licensing factor MCM7 (EC 3.6.4.12)	protein	601	31% helix, 15% strand	Q9XYU0

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains 6, 4, 5, 3, 7
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 2, 5, 6

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	1000	0.89	0.91	139	ATP
2	794	0.89	0.93	125	ATP
3	783	0.89	0.93	131	empty
4	740	0.88	0.92	120	ATP
5	759	0.88	0.91	101	empty

Interfaces

28 interfaces between chains.

4–7 · 3477 Å² buried · 40 hydrogen bonds · protein-protein
2–5 · 3172 Å² buried · 42 hydrogen bonds · protein-protein
6–4 · 3075 Å² buried · 41 hydrogen bonds · protein-protein
3–7 · 2892 Å² buried · 28 hydrogen bonds · protein-protein
5–3 · 2560 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

6RAZ · D. melanogaster CMG-DNA, State 2B · the same entry in another collection · chain 7 against 7, 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 O96989
Every structure of UniProt Q9W0I7
Every structure of UniProt Q9VQY9
Every structure of UniProt Q9W2V7
Every structure of UniProt Q9VBI1
Every structure of UniProt P49735
Every structure of UniProt Q9VGW6
Every structure of UniProt Q9V461
Every structure of UniProt Q9XYU1
Every structure of UniProt Q26454
Every structure of UniProt Q9XYU0
Elsewhere: RCSB PDB 6RAZ · PDBe 6RAZ · UniProt O96989 · UniProt Q9W0I7 · UniProt Q9VQY9 · UniProt Q9W2V7 · UniProt Q9VBI1 · UniProt P49735 · UniProt Q9VGW6 · UniProt Q9V461 · UniProt Q9XYU1 · UniProt Q26454 · UniProt Q9XYU0

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