MolNFT v1 · #77460 · protein

Crystal structure of particulate methane monooxygenase (pmmo) from methylocystis sp. strain M

3RFR · Pmob: “Crystal structure of particulate methane monooxygenase (pmmo) from methylocystis sp. strain M”. X-ray diffraction, 3 ligands (CUA, ZN, CU), 20 pockets (best druggability 0.82). MolNFT v1 #77460 on GenesisL1: 3D structure…

PDB: 3RFR
Type: protein
Length: 2,551 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pmob; Peptide; Pmoa; Pmoc
UniProt: Q9KX36, O06122, Q9KX37
Ligands: CUA, ZN, CU
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	Pmob	protein	386	20% helix, 36% strand	Q9KX36
D	Peptide	protein	19	53% helix, 0% strand	—
H	Peptide	protein	16	69% helix, 0% strand	—
J, B, F	Pmoa	protein	242	67% helix, 4% strand	O06122
C	Pmoc	protein	210	70% helix, 1% strand	Q9KX37
G, K	Pmoc	protein	211	69% helix, 1% strand	Q9KX37

Ligands and binding sites

CUA · Dinuclear copper ion · ligand · chains A
ZN · Zinc ion · metal · 9 copies · chains A, C, G, K, E, I
CU · Copper (II) ion · metal · 2 copies · chains E, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	847	0.82	0.84	97	empty
2	849	0.82	0.84	100	empty
3	706	0.80	0.84	89	empty
4	622	0.77	0.82	54	empty
5	64	0.72	0.97	26	empty

Interfaces

23 interfaces between chains.

J–I · 3947 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 3934 Å² buried · 31 hydrogen bonds · protein-protein
F–E · 3917 Å² buried · 31 hydrogen bonds · protein-protein
J–K · 2896 Å² buried · 32 hydrogen bonds · protein-protein
F–G · 2858 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

3RFR · Crystal Structure of particulate methane monooxygenase (pMMO) from Methylocystis sp.… · the same entry in another collection · chain B against B, 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 Q9KX36
Every structure of UniProt O06122
Every structure of UniProt Q9KX37
Elsewhere: RCSB PDB 3RFR · PDBe 3RFR · UniProt Q9KX36 · UniProt O06122 · UniProt Q9KX37

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