SMTL ID : 7lc0.1

Structure of D-Glucosaminate-6-phosphate Ammonia-lyase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-octamer

Ligands

19 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 3 residues within 4Å: Chain A: H.87, T.228, W.229 Ligand excluded by PLIP DMS.3: 4 residues within 4Å: Chain A: I.172, D.195, G.198, W.199 Ligand excluded by PLIP DMS.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.7: 3 residues within 4Å: Chain B: V.255, Y.256, E.259 Ligand excluded by PLIP DMS.8: 2 residues within 4Å: Chain B: H.87, W.229 Ligand excluded by PLIP DMS.12: 2 residues within 4Å: Chain C: H.87, R.92 Ligand excluded by PLIP DMS.14: 2 residues within 4Å: Chain D: H.87, T.228 Ligand excluded by PLIP DMS.15: 2 residues within 4Å: Chain D: Y.256, E.259 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain D: D.195, G.198, W.199 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain E: L.9 Chain G: V.255, Y.256 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain E: H.87, T.228, W.229 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain E: H.183, L.184, D.205, R.226, W.229 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain F: Y.61, V.255, Y.256, E.259 Ligand excluded by PLIP DMS.25: 1 residues within 4Å: Chain F: R.92 Ligand excluded by PLIP DMS.26: 3 residues within 4Å: Chain F: H.87, T.228, W.229 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain F: H.183, L.184, D.205, W.229 Ligand excluded by PLIP DMS.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain G: Q.180, G.203, D.205, R.226 Ligand excluded by PLIP DMS.31: 3 residues within 4Å: Chain G: E.146, I.149, N.182 Ligand excluded by PLIP

5 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 4 residues within 4Å: Chain A: R.90 Chain B: R.142, W.143, E.146 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.142 Salt bridges: A:R.90 ACY.5: 4 residues within 4Å: Chain B: E.32, Q.35, R.39, Y.256 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.256 Salt bridges: B:R.39 ACY.17: 4 residues within 4Å: Chain E: R.39, Y.256 Chain G: I.5, Q.8 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.39 ACY.18: 2 residues within 4Å: Chain E: N.150, N.182 No protein-ligand interaction detected (PLIP) ACY.19: 5 residues within 4Å: Chain E: N.113, T.121 Chain F: R.110, G.135, S.136 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Water bridges: F:R.110 Salt bridges: F:R.110 Hydrogen bonds: E:N.113, E:T.121

11 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: S.281, A.282 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.281 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain E: G.198 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain F: W.199 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain C: N.113, T.121 Chain G: R.110 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain G: G.198 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain G: H.87 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain H: W.199 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain H: T.228 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain H: E.52 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain B: N.113, T.121 Chain H: R.110 Ligand excluded by PLIP

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

PEG.11: 5 residues within 4Å: Chain C: Q.321, E.326, R.359, E.362, H.366 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.321, C:E.326, C:R.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid. Biochemistry (2021)

Release Date

2021-06-09

Peptides

Putative selenocysteine synthase (L-seryl-tRNA(Ser) selenium transferase): ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Putative selenocysteine synthase (L-seryl-tRNA(Ser) selenium transferase)

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