SMTL ID : 4rit.1

The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.399, L.400 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: T.314, H.356 Chain B: T.314, H.356 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: R.399, L.400 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: P.460, Y.461 Chain B: L.9 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:P.10, B:A.11, A:D.380, A:D.380, A:Y.461 GOL.4: 9 residues within 4Å: Chain A: Y.310, L.377, D.380, G.381, L.384, L.457, L.458, N.459, P.460 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.310, A:Y.310 Water bridges: A:R.376, A:D.380, A:N.407, A:N.459, A:T.462 GOL.5: 4 residues within 4Å: Chain A: W.363 Chain B: A.74, D.77, M.78 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.367, A:Q.367 Hydrogen bonds: B:A.74 GOL.6: 4 residues within 4Å: Chain A: R.412, A.420, W.423, G.450 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.412, A:R.412, A:A.420 Water bridges: A:W.423, A:R.448 GOL.7: 7 residues within 4Å: Chain A: R.387, E.390, G.391, Q.394, R.395, D.468, F.471 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.390, A:E.390, A:Q.394, A:R.395, A:D.468, A:D.468 Water bridges: A:R.395 GOL.11: 6 residues within 4Å: Chain B: T.130, G.147, G.148, A.323, L.346, I.349 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.148, B:G.148 Water bridges: B:R.134, B:R.134, B:G.148, B:E.327, B:E.327 GOL.12: 4 residues within 4Å: Chain B: R.127, L.131, R.134, F.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.127, B:R.134, B:R.134, B:F.343 Water bridges: B:I.344 GOL.13: 10 residues within 4Å: Chain B: Y.310, L.377, D.380, G.381, L.384, L.457, L.458, N.459, P.460, T.462 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.310, B:G.381, B:L.457 Water bridges: B:N.407 GOL.14: 5 residues within 4Å: Chain B: R.387, E.390, G.391, D.468, F.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.390, B:I.467 Water bridges: B:R.395, B:R.395 GOL.15: 5 residues within 4Å: Chain A: Q.431, F.441, S.443, L.444 Chain B: E.120 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.431, A:L.444, B:E.120 GOL.16: 3 residues within 4Å: Chain B: G.269, L.270, D.299 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.269 Water bridges: B:W.271, B:F.272, B:D.299, B:D.299, B:D.299, B:D.299

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

TRS.8: 6 residues within 4Å: Chain A: L.139, F.140, G.141, R.289, L.292, E.296 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.140, A:R.289, A:R.289, A:E.296 Water bridges: A:R.289 TRS.9: 5 residues within 4Å: Chain A: V.168, G.269, L.270, W.271, D.299 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.299 Water bridges: A:F.241, A:F.241, A:G.269, A:F.272 TRS.17: 10 residues within 4Å: Chain B: L.139, F.140, G.141, R.289, W.290, L.292, A.293, G.294, I.295, E.296 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.139, B:R.289, B:G.294, B:E.296, B:E.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745. To be Published

Release Date

2014-10-22

Peptides

Pyridoxal-dependent decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Pyridoxal-dependent decarboxylase

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