MolNFT v1 · #137371 · protein

Staphylococcus aureus isdb bound to human hemoglobin

5VMM · Hemoglobin subunit alpha: “Staphylococcus aureus isdb bound to human hemoglobin”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.84). MolNFT v1 #137371 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5VMM
Type: protein
Length: 1,470 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit alpha; Hemoglobin subunit beta; Iron-regulated cell wall-anchored…
UniProt: P69905, P68871, A0A1K8PKR3
Ligands: HEM
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 8 distinct chains · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemoglobin subunit alpha	protein	139	78% helix, 0% strand	P69905
B	Hemoglobin subunit beta	protein	132	72% helix, 0% strand	P68871
C	Hemoglobin subunit alpha	protein	141	65% helix, 0% strand	P69905
D	Hemoglobin subunit beta	protein	128	73% helix, 0% strand	P68871
E	Iron-regulated cell wall-anchored protein	protein	329	20% helix, 36% strand	A0A1K8PKR3
F	Iron-regulated cell wall-anchored protein	protein	325	22% helix, 40% strand	A0A1K8PKR3
H	Iron-regulated cell wall-anchored protein	protein	141	6% helix, 45% strand	A0A1K8PKR3
J	Iron-regulated cell wall-anchored protein	protein	135	8% helix, 44% strand	A0A1K8PKR3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, F, C, E

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	799	0.84	0.86	65	HEM
2	909	0.84	0.86	84	empty
3	1090	0.83	0.84	79	HEM
4	540	0.70	0.79	61	empty
5	437	0.66	0.79	62	empty

Interfaces

14 interfaces between chains.

C–E · 1728 Å² buried · 16 hydrogen bonds · protein-protein
A–F · 1690 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 942 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 892 Å² buried · 9 hydrogen bonds · protein-protein
B–H · 738 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5VMM · Staphylococcus aureus IsdB bound to human hemoglobin · the same entry in another collection · chain A against A, 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 P69905
Every structure of UniProt P68871
Every structure of UniProt A0A1K8PKR3
Elsewhere: RCSB PDB 5VMM · PDBe 5VMM · UniProt P69905 · UniProt P68871 · UniProt A0A1K8PKR3

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