SMTL ID : 6qwv.2 (1 other biounit)

SARM1 SAM1-2 domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-octamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.65, E.66, D.70 Chain B: G.76 Ligand excluded by PLIP EDO.2: 8 residues within 4Å: Chain A: A.93, N.94, Y.95, S.96, D.99, N.102, A.104, R.115 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain B: L.62, T.63, F.83, K.90, H.146 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain B: A.93, N.94, Y.95, S.96, D.99, N.102, A.104, R.115 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: L.60, R.61, Y.119, G.120, C.143 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: K.44, Y.45, S.48, L.71, G.72 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain B: K.44 Ligands: EDO.10 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: Q.116, L.147, H.150 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain C: L.62, F.83, K.90 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain C: D.55 Chain D: R.84 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain C: A.93, N.94, Y.95, S.96, D.99, N.102, A.104, R.115 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: L.130, R.133, Q.138 Chain D: V.149, R.153 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain D: K.44, Y.45, S.48, L.71, G.72 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain D: T.69, D.70 Chain E: K.74, S.75 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: H.146, R.151 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain E: S.24, S.27, W.28, K.29, E.32 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain E: A.93, N.94, Y.95, S.96, D.99, N.102, A.104, R.115 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain E: D.105, R.128 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain D: S.123 Chain E: Q.116, H.150 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain F: E.64, F.83, H.146 Ligand excluded by PLIP EDO.30: 1 residues within 4Å: Chain G: R.128 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain G: D.55, D.57 Ligands: BME.31 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain G: L.62, F.83, K.90 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain G: Q.53 Chain H: G.41, F.42, K.44, Y.45, R.81 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain H: K.44, S.48, L.71, G.72 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain H: R.61, C.143 Ligand excluded by PLIP

8 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 4 residues within 4Å: Chain A: C.98, Y.119, V.122, S.123 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.113, A:V.122 BME.9: 4 residues within 4Å: Chain B: C.98, Y.119, S.123 Chain C: R.113 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.57, B:D.57, B:Y.119 BME.14: 4 residues within 4Å: Chain C: C.98, Y.119, V.122, S.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.122 BME.20: 3 residues within 4Å: Chain D: C.98, Y.119, S.123 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.123 BME.23: 3 residues within 4Å: Chain E: C.98, Y.119, S.123 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.123 BME.28: 3 residues within 4Å: Chain F: C.98, V.122, S.123 2 PLIP interactions: 2 interactions with chain F Water bridges: F:D.57, F:S.123 BME.31: 6 residues within 4Å: Chain G: C.98, Y.119, V.122, S.123 Chain H: R.113 Ligands: EDO.32 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:S.123, H:R.113 BME.36: 5 residues within 4Å: Chain H: C.98, Y.119, V.122, S.123 Ligands: PGE.37 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.122

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: Q.53 Chain B: G.41, F.42, K.44, Y.45, T.78, R.81 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.81, B:R.81 Water bridges: A:Q.52, A:Q.53, A:Q.53 PEG.5: 6 residues within 4Å: Chain B: P.20, W.28, E.32, T.35, W.36, Q.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.35, B:W.36, B:Q.39 PEG.15: 6 residues within 4Å: Chain C: P.23, S.24, S.27, W.28, K.29, E.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.24, C:S.27

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.37: 6 residues within 4Å: Chain A: R.84 Chain H: D.55, D.57, R.61, S.123 Ligands: BME.36 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:R.61 Water bridges: H:D.57, H:Y.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sporny, M. et al., Structural Evidence for an Octameric Ring Arrangement of SARM1. J.Mol.Biol. (2019)

Release Date

2019-07-03

Peptides

Sterile alpha and TIR motif-containing protein 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

Sterile alpha and TIR motif-containing protein 1

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