SMTL ID : 7lce.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-octamer

Ligands

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

DMS.1: 2 residues within 4Å: Chain A: Q.180, H.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.180 DMS.2: 1 residues within 4Å: Chain A: H.87 No protein-ligand interaction detected (PLIP) DMS.3: 3 residues within 4Å: Chain A: Q.180, S.202, G.203 No protein-ligand interaction detected (PLIP) DMS.10: 3 residues within 4Å: Chain B: N.150, N.182, L.184 No protein-ligand interaction detected (PLIP) DMS.15: 6 residues within 4Å: Chain A: N.113, P.119, T.121 Chain C: R.110, G.135, S.136 No protein-ligand interaction detected (PLIP) DMS.19: 2 residues within 4Å: Chain D: E.46, D.48 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:E.46, D:D.48 DMS.23: 2 residues within 4Å: Chain E: Q.180, H.183 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.180 DMS.24: 1 residues within 4Å: Chain E: H.87 No protein-ligand interaction detected (PLIP) DMS.25: 3 residues within 4Å: Chain E: Q.180, S.202, G.203 No protein-ligand interaction detected (PLIP) DMS.32: 3 residues within 4Å: Chain F: N.150, N.182, L.184 No protein-ligand interaction detected (PLIP) DMS.37: 6 residues within 4Å: Chain E: N.113, P.119, T.121 Chain G: R.110, G.135, S.136 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.121 DMS.41: 2 residues within 4Å: Chain H: E.46, D.48 2 PLIP interactions: 2 interactions with chain H Salt bridges: H:E.46, H:D.48

32 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain A: E.310 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.310, A:E.310, H2O.1 CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain A: I.290 No protein-ligand interaction detected (PLIP) CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain B: H.87 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain B: N.314, D.317 No protein-ligand interaction detected (PLIP) CA.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 2 residues within 4Å: Chain C: H.87, T.228 No protein-ligand interaction detected (PLIP) CA.18: 1 residues within 4Å: Chain C: N.182 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain D: H.87, T.228 No protein-ligand interaction detected (PLIP) CA.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.27: 1 residues within 4Å: Chain E: E.310 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.310, E:E.310, H2O.7 CA.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.30: 1 residues within 4Å: Chain E: I.290 No protein-ligand interaction detected (PLIP) CA.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.34: 1 residues within 4Å: Chain F: H.87 No protein-ligand interaction detected (PLIP) CA.35: 2 residues within 4Å: Chain F: N.314, D.317 No protein-ligand interaction detected (PLIP) CA.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.39: 2 residues within 4Å: Chain G: H.87, T.228 No protein-ligand interaction detected (PLIP) CA.40: 1 residues within 4Å: Chain G: N.182 No protein-ligand interaction detected (PLIP) CA.42: 2 residues within 4Å: Chain H: H.87, T.228 No protein-ligand interaction detected (PLIP) CA.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

D-glucosaminate-6-phosphate ammonia lyase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

D-glucosaminate-6-phosphate ammonia lyase

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