SMTL ID : 3mbb.1

Crystal structure of StSPL - apo form, after treatment with semicarbazide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.103, A.104, Y.106, K.312 Chain B: N.127, L.129, H.130, S.354 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.104, A:Y.106, B:N.127 Water bridges: A:Y.106, A:Y.106, A:K.312, B:S.354, B:S.354 Salt bridges: A:K.312, A:K.318, B:H.130 PO4.2: 8 residues within 4Å: Chain A: G.169, T.170, Y.250, D.309, H.311, K.312 Chain B: G.353, S.354 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.353, B:S.354, A:G.169, A:T.170, A:T.170, A:D.309 Water bridges: B:S.354, B:S.354, A:K.312, A:K.312 Salt bridges: A:H.311, A:K.312 PO4.5: 8 residues within 4Å: Chain A: N.127, L.129, H.130, S.354 Chain B: G.103, A.104, Y.106, K.312 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:N.127, B:A.104, B:Y.106 Water bridges: A:S.354, A:S.354, B:K.312, B:K.318, B:K.318 Salt bridges: A:H.130, B:K.312, B:K.318 PO4.6: 8 residues within 4Å: Chain A: G.353, S.354 Chain B: G.168, G.169, T.170, D.309, H.311, K.312 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.169, B:T.170, A:G.353, A:S.354, A:S.354 Water bridges: B:T.170, B:T.170, B:T.170, B:T.170, B:H.202, B:K.312, B:K.312, A:S.354, A:S.354 Salt bridges: B:H.311, B:K.312

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: A.121, L.122, Q.123, S.124, Q.125 Chain B: I.113, N.117 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.117, A:Q.125 Water bridges: B:R.97

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: V.393, R.394, I.396, L.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bourquin, F. et al., Structure and Function of Sphingosine-1-Phosphate Lyase, a Key Enzyme of Sphingolipid Metabolism. Structure (2010)

Release Date

2010-08-18

Peptides

Putative sphingosine-1-phosphate lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative sphingosine-1-phosphate lyase

Related Entries With Identical Sequence