SMTL ID : 4xg1.1 (1 other biounit)

Psychromonas ingrahamii diaminopimelate decarboxylase with LLP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

6 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 5 residues within 4Å: Chain A: N.383, S.386, L.412 Chain B: R.89 Ligands: K.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.89 SCN.2: 5 residues within 4Å: Chain A: P.346, N.385, R.387 Chain B: V.82, S.83 No protein-ligand interaction detected (PLIP) SCN.3: 8 residues within 4Å: Chain A: V.82, F.102, G.104, V.105, G.106, K.107, E.111 Chain B: P.346 No protein-ligand interaction detected (PLIP) SCN.4: 2 residues within 4Å: Chain A: Q.92 Chain B: W.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.92 SCN.9: 6 residues within 4Å: Chain B: R.150, F.172, H.200, G.202, S.203 Ligands: LLP.16 No protein-ligand interaction detected (PLIP) SCN.10: 7 residues within 4Å: Chain B: P.325, L.326, Y.330, A.361, L.362, D.366, Y.367 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: A.186, S.187, L.189, L.192 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.189, A:L.192, H2O.2 K.6: 2 residues within 4Å: Chain A: H.417, I.418 No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain B: A.186, S.187, L.189, L.192 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.192, H2O.6 K.12: 2 residues within 4Å: Chain B: S.378 Ligands: SCN.1 No protein-ligand interaction detected (PLIP)

4 x TME: PROPANE(Non-covalent)(Non-functional Binders)

TME.7: 6 residues within 4Å: Chain A: S.127, I.128, S.129, I.174 Chain B: L.293, K.294 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.128, A:I.128, A:I.128, A:I.174, B:K.294 TME.13: 3 residues within 4Å: Chain B: E.207, I.208, A.209 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.208, B:A.209 TME.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TME.15: 3 residues within 4Å: Chain B: A.36, E.39, R.40 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.39, B:R.40

2 x LLP: (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid(Non-covalent)

LLP.8: 18 residues within 4Å: Chain A: K.61, D.80, S.103, H.200, S.203, G.239, G.240, E.274, P.275, G.276, R.277, R.313, Y.317, Y.376, M.380 Chain B: C.348, E.349, Y.384 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.61, A:Y.376, A:Y.376, B:E.349 Hydrogen bonds: A:G.240, A:E.274, A:G.276, A:R.277, A:R.277, A:Y.376, A:Y.376, B:E.349 Water bridges: A:L.241, A:L.241 Salt bridges: A:R.277, A:R.313 pi-Stacking: A:H.200 LLP.16: 20 residues within 4Å: Chain A: C.348, E.349, Y.384 Chain B: A.59, K.61, D.80, S.103, H.200, S.203, G.239, G.240, E.274, P.275, G.276, R.277, R.313, Y.317, Y.376, M.380 Ligands: SCN.9 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.61, B:H.200, A:E.349 Hydrogen bonds: B:S.203, B:G.240, B:G.276, B:R.277, B:Y.317, B:Y.376, A:E.349 Water bridges: B:L.241, B:R.277 Salt bridges: B:R.277, B:R.277, B:R.313 pi-Stacking: B:H.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peverelli, M.G. et al., Expression to crystallization of diaminopimelate decarboxylase from the psychrophile Psychromonas ingrahamii. To Be Published

Release Date

2016-03-09

Peptides

Diaminopimelate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diaminopimelate decarboxylase

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