MolNFT v1 · #188076 · protein

Crystal structure of the PBP2_YVGL_LIKE protein LMO1041 from listeria monocytogene

7TAV · Molybdate ABC transporter substrate-binding protein: “Crystal structure of the PBP2_YVGL_LIKE protein LMO1041 from listeria monocytogene”. X-ray diffraction, 3 ligands (CA, SO4, CL), 13 pockets (best druggability 0.74). MolNFT v1…

PDB: 7TAV
Type: protein
Length: 1,351 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Molybdate ABC transporter substrate-binding protein
UniProt: A0A5D5LL32
Ligands: CA, SO4, CL
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 41% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Molybdate ABC transporter substrate-binding protein	protein	225	41% helix, 28% strand	A0A5D5LL32
B	Molybdate ABC transporter substrate-binding protein	protein	229	41% helix, 27% strand	A0A5D5LL32
C, D	Molybdate ABC transporter substrate-binding protein	protein	224	42% helix, 28% strand	A0A5D5LL32
E	Molybdate ABC transporter substrate-binding protein	protein	223	40% helix, 28% strand	A0A5D5LL32
F	Molybdate ABC transporter substrate-binding protein	protein	226	42% helix, 27% strand	A0A5D5LL32

Ligands and binding sites

CA · Calcium ion · metal · 18 copies · chains A, C, D, B, E, F
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B, F

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.74	0.77	81	GOL, CL
2	934	0.73	0.77	81	GOL
3	480	0.73	0.83	67	CA
4	718	0.72	0.78	69	empty
5	834	0.66	0.73	88	CA

Interfaces

8 interfaces between chains.

A–B · 981 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 966 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 933 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 408 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 371 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7TAV · Crystal Structure of the PBP2_YvgL_like protein Lmo1041 from Listeria monocytogene · the same entry in another collection · chain C against C, 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 A0A5D5LL32
Elsewhere: RCSB PDB 7TAV · PDBe 7TAV · UniProt A0A5D5LL32

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