SMTL ID : 6wng.1

Crystal structure of an aspartate ammonia-lyase from Elizabethkingia anophelis NUHP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 9 residues within 4Å: Chain A: A.308, I.318, N.319, L.320, K.322, V.334, N.335, P.336 Chain D: Q.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.318, A:L.320, A:L.320 Water bridges: A:N.319 TRS.7: 9 residues within 4Å: Chain B: A.308, I.318, N.319, L.320, K.322, V.334, N.335, P.336 Chain C: Q.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.318, B:L.320, B:P.321, B:N.335 TRS.13: 9 residues within 4Å: Chain B: Q.199 Chain C: A.308, I.318, N.319, L.320, K.322, V.334, N.335, P.336 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.318, C:L.320, C:L.320 Water bridges: C:N.319 TRS.19: 9 residues within 4Å: Chain A: Q.199 Chain D: A.308, I.318, N.319, L.320, K.322, V.334, N.335, P.336 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:I.318, D:L.320, D:V.334 Water bridges: D:N.319, A:Q.199, A:Q.199

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 13 residues within 4Å: Chain A: G.326, S.327, S.328, I.329, M.330, K.333, N.335 Chain B: T.110, S.149, T.150, N.151 Chain D: T.196, Q.197 10 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:G.326, A:G.326, A:S.328, A:I.329, A:N.335, B:T.150, B:T.150, B:N.151, D:T.196 Salt bridges: A:K.333 FUM.8: 14 residues within 4Å: Chain A: T.110, S.149, T.150, N.151, L.367 Chain B: G.326, S.327, S.328, I.329, M.330, K.333, N.335 Chain C: T.196, Q.197 9 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: B:G.326, B:S.328, B:I.329, B:N.335, C:T.196, A:T.110, A:T.150, A:N.151 Salt bridges: B:K.333 FUM.14: 14 residues within 4Å: Chain B: T.196, Q.197 Chain C: G.326, S.327, S.328, I.329, M.330, K.333, N.335 Chain D: T.110, S.149, T.150, N.151, L.367 10 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: D:S.149, D:T.150, D:T.150, D:N.151, D:N.151, B:T.196, C:S.328, C:I.329, C:N.335 Salt bridges: C:K.333 FUM.20: 13 residues within 4Å: Chain A: T.196, Q.197 Chain C: T.110, S.149, T.150, N.151 Chain D: G.326, S.327, S.328, I.329, M.330, K.333, N.335 9 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:S.328, D:I.329, D:N.335, C:S.149, C:T.150, C:N.151, C:N.151, A:T.196 Salt bridges: D:K.333

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: S.16, D.17, V.32, Q.33, M.114, E.118, Y.135 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.33, A:E.118 Water bridges: A:S.16, A:S.16, A:S.16, A:N.141, A:N.141 GOL.9: 8 residues within 4Å: Chain B: S.16, D.17, V.32, Q.33, M.114, E.118, Y.135, P.140 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.33, B:E.118 Water bridges: B:S.16, B:N.141, B:N.141 GOL.15: 8 residues within 4Å: Chain C: S.16, D.17, V.32, Q.33, M.114, E.118, Y.135, P.140 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.33, C:E.118 Water bridges: C:S.16, C:N.141 GOL.21: 8 residues within 4Å: Chain D: S.16, D.17, V.32, Q.33, M.114, E.118, Y.135, P.140 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.33, D:E.118, D:E.118 Water bridges: D:S.16, D:N.141, D:N.141

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

CL.4: 5 residues within 4Å: Chain A: Q.197 Chain C: V.369 Chain D: R.305, P.336, E.340 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.383, K.386 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: H.51, P.52, E.53, L.165 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: Q.197 Chain C: R.305, P.336, E.340 Chain D: V.369 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.383, K.386 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: H.51, P.52, E.53, L.165 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: V.369 Chain B: R.305, P.336, E.340 Chain C: Q.197 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: R.383, K.386 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: H.51, P.52, E.53, L.165 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: R.305, P.336, E.340 Chain B: V.369 Chain D: Q.197 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain D: R.383, K.386 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain D: H.51, P.52, E.53, L.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of an aspartate ammonia-lyase from Elizabethkingia anophelis NUHP1. To Be Published

Release Date

2020-04-29

Peptides

Aspartate ammonia-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aspartate ammonia-lyase