SMTL ID : 4mzy.1

Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase with malonate and phosphate bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: H.225, R.226, D.227 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.226, A:D.227, A:D.227 Salt bridges: A:H.225 Water bridges: B:Q.23, B:Q.23 PO4.2: 5 residues within 4Å: Chain A: N.293, D.294, V.315, G.316, T.317 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.164, A:N.293, A:D.294, A:G.316, A:T.317, A:T.317 Water bridges: A:L.295, A:L.295, A:K.318 PO4.23: 3 residues within 4Å: Chain B: H.225, R.226, D.227 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.226, B:D.227, B:D.227 Salt bridges: B:H.225 Water bridges: A:Q.23, A:Q.23 PO4.24: 5 residues within 4Å: Chain B: N.293, D.294, V.315, G.316, T.317 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.164, B:N.293, B:D.294, B:G.316, B:T.317, B:T.317 Water bridges: B:L.295, B:L.295, B:K.318

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: Y.179, I.180, G.181, G.182, K.437, A.440, K.441, L.444 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: L.103, E.104, Y.428, P.431, I.436, Y.439 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: M.396, H.398, I.404, N.405, K.406, P.461, D.463 Ligands: GOL.13 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: S.150, R.453, D.454, L.455 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: D.236, T.237, L.238, K.239, I.271 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: Q.364, W.366, W.384, E.386, D.387, R.389 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: V.479, D.482, L.486 Chain B: G.212, N.213 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: K.149, D.154, D.184 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: E.57, N.61, I.194 Chain B: D.7 Ligands: MLA.16 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: L.63, E.64, L.66, T.67, E.94, F.95 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: N.110, H.398, K.459, Y.460, P.461, V.462, D.463 Ligands: GOL.5 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: D.155, K.309, I.310, D.311 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain B: Y.179, I.180, G.181, G.182, K.437, A.440, K.441, L.444 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: L.103, E.104, Y.428, P.431, I.436, Y.439 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain B: M.396, H.398, I.404, N.405, K.406, P.461, D.463 Ligands: GOL.35 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain B: S.150, R.453, D.454, L.455 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: D.236, T.237, L.238, K.239, I.271 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain B: Q.364, W.366, W.384, E.386, D.387, R.389 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain A: G.212, N.213 Chain B: V.479, D.482, L.486 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain B: K.149, D.154, D.184 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain A: D.7 Chain B: E.57, N.61, I.194 Ligands: MLA.38 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain B: L.63, E.64, L.66, T.67, E.94, F.95 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain B: N.110, H.398, K.459, Y.460, P.461, V.462, D.463 Ligands: GOL.27 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain B: D.155, K.309, I.310, D.311 Ligand excluded by PLIP

6 x MLA: MALONIC ACID(Non-covalent)

MLA.15: 8 residues within 4Å: Chain A: A.204, H.205, S.206 Chain B: Q.125, E.128, F.332, K.333 Ligands: FMT.20 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.205, A:S.206, B:Q.125 Water bridges: A:R.163 Salt bridges: A:H.205, B:K.333, B:K.333 MLA.16: 7 residues within 4Å: Chain A: R.58, D.169, I.172, W.173, R.190 Chain B: D.7 Ligands: GOL.11 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:D.7, B:D.7, B:D.7 Hydrophobic interactions: A:W.173 Water bridges: A:R.58, A:R.58, A:R.58, A:R.58, A:R.190, A:R.190 Salt bridges: A:R.58, A:R.190 MLA.17: 6 residues within 4Å: Chain A: E.38, Y.40, P.113, T.358, T.359, K.363 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.40 Hydrogen bonds: A:E.38, A:T.359, A:T.359 Water bridges: A:N.111, A:N.111 Salt bridges: A:K.363, A:K.472 MLA.37: 8 residues within 4Å: Chain A: Q.125, E.128, F.332, K.333 Chain B: A.204, H.205, S.206 Ligands: FMT.42 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.205, B:S.206, A:Q.125 Water bridges: B:R.163 Salt bridges: B:H.205, A:K.333, A:K.333 MLA.38: 7 residues within 4Å: Chain A: D.7 Chain B: R.58, D.169, I.172, W.173, R.190 Ligands: GOL.33 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.173 Water bridges: B:R.58, B:R.58, B:R.58, B:R.58, B:R.190, B:R.190 Salt bridges: B:R.58, B:R.190 Hydrogen bonds: A:D.7, A:D.7, A:D.7 MLA.39: 6 residues within 4Å: Chain B: E.38, Y.40, P.113, T.358, T.359, K.363 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.40 Hydrogen bonds: B:E.38, B:T.359, B:T.359 Water bridges: B:N.111, B:N.111 Salt bridges: B:K.363, B:K.472

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

CL.18: 5 residues within 4Å: Chain A: R.163, R.164 Chain B: L.132, V.331, F.332 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain A: R.274 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: G.201, T.202 Chain B: Y.17 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: S.200, G.201 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain A: L.132, V.331, F.332 Chain B: R.163, R.164 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain B: R.274 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain A: Y.17 Chain B: G.201, T.202 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain B: S.200, G.201 Ligand excluded by PLIP

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.20: 3 residues within 4Å: Chain A: A.204, R.262 Ligands: MLA.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.262, A:R.262 FMT.42: 3 residues within 4Å: Chain B: A.204, R.262 Ligands: MLA.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.262, B:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase. To be Published

Release Date

2013-10-23

Peptides

NICOTINATE PHOSPHORIBOSYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NICOTINATE PHOSPHORIBOSYLTRANSFERASE

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