MolNFT v1 · #107910 · protein

Methanococcus jannaschii serine hydroxymethyl-transferase in complex with plp

4UQV · Serine hydroxymethyltransferase: “Methanococcus jannaschii serine hydroxymethyl-transferase in complex with plp”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.87). MolNFT v1 #107910 on GenesisL1: 3D structure…

PDB: 4UQV
Type: protein
Length: 5,094 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine hydroxymethyltransferase
EC: 2.1.2.-, 4.1.2.49
UniProt: Q58992
Ligands: PLP
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 10 distinct chains · 40% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	426	41% helix, 12% strand	Q58992
B	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	424	42% helix, 12% strand	Q58992
C	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	420	40% helix, 11% strand	Q58992
D	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	425	37% helix, 10% strand	Q58992
E, I	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	427	41% helix, 10% strand	Q58992
F	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	418	41% helix, 12% strand	Q58992
G, J	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	429	39% helix, 11% strand	Q58992
H	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	427	37% helix, 12% strand	Q58992
K	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	422	37% helix, 12% strand	Q58992
L	Serine hydroxymethyltransferase (EC 2.1.2.-, 4.1.2.49)	protein	420	40% helix, 11% strand	Q58992

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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	1179	0.87	0.88	143	PLP
2	430	0.86	0.93	61	PLP
3	1194	0.83	0.84	125	PLP
4	912	0.82	0.84	97	empty
5	1192	0.81	0.82	102	empty

Interfaces

21 interfaces between chains.

K–L · 4721 Å² buried · 65 hydrogen bonds · protein-protein
A–B · 4600 Å² buried · 43 hydrogen bonds · protein-protein
G–H · 4556 Å² buried · 52 hydrogen bonds · protein-protein
C–D · 4538 Å² buried · 49 hydrogen bonds · protein-protein
E–F · 4472 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 cofactor (pyridoxal phosphate Schiff base).

Compared structures

4UQV · methanococcus jannaschii serine hydroxymethyl-transferase in complex with PLP · the same entry in another collection · chain L against L, 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 Q58992
Elsewhere: RCSB PDB 4UQV · PDBe 4UQV · UniProt Q58992

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