MolNFT v1 · #139905 · protein

Crystal structure of the cysr-CTLD2 fragment of human mr at acidic pH

5XTW · Macrophage mannose receptor 1: “Crystal structure of the cysr-CTLD2 fragment of human mr at acidic pH”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.74). MolNFT v1 #139905 on GenesisL1: 3D structure, binding…

PDB: 5XTW
Type: protein
Length: 3,540 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrophage mannose receptor 1
UniProt: P22897
Ligands: CA
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 15% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Macrophage mannose receptor 1	protein	443	15% helix, 35% strand	P22897
C	Macrophage mannose receptor 1	protein	441	15% helix, 34% strand	P22897
E	Macrophage mannose receptor 1	protein	444	15% helix, 34% strand	P22897
F	Macrophage mannose receptor 1	protein	442	15% helix, 36% strand	P22897
G	Macrophage mannose receptor 1	protein	443	15% helix, 34% strand	P22897
H	Macrophage mannose receptor 1	protein	441	15% helix, 34% strand	P22897

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains A, C, D, E, F, H
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	881	0.74	0.78	71	empty
2	734	0.71	0.77	82	empty
3	645	0.71	0.78	48	CA
4	448	0.67	0.79	66	empty
5	401	0.66	0.79	53	empty

Interfaces

8 interfaces between chains.

C–D · 662 Å² buried · 11 hydrogen bonds · protein-protein
E–G · 644 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 624 Å² buried · 1 hydrogen bond · protein-protein
C–H · 507 Å² buried · 2 hydrogen bonds · protein-protein
A–G · 317 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 72 disulfide (disulfide).

Compared structures

5XTW · Crystal structure of the CysR-CTLD2 fragment of human MR at acidic pH · the same entry in another collection · chain H against H, TM-score 1.00
P22897 · AlphaFold monomer V2.0 prediction for macrophage mannose receptor 1 (P22897) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 P22897
Elsewhere: RCSB PDB 5XTW · PDBe 5XTW · UniProt P22897

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