SMTL ID : 8q3s.1

HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x GLY- ASN- CYS- PHE- SER- LYS- ALA- ARG: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG(Non-covalent)

GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG.1: 27 residues within 4Å: Chain A: Y.85, V.86, E.87, D.88, D.90, F.93, F.95, Y.97, N.151, T.187, A.188, G.189, Y.201, H.203, F.216, S.217, Y.306, S.310, I.374, G.375, D.376, G.377, N.378, L.379, Q.401 Ligands: COA.3, MYR.11 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:D.88, A:F.93, A:F.93, A:F.95, A:F.95, A:F.216 Hydrogen bonds: A:Y.85, A:D.88, A:D.90, A:D.90, A:T.187, A:T.187, A:Y.201, A:F.216, A:Y.306, A:I.374, A:D.376, A:D.376, A:D.376, A:D.376, A:G.377, A:G.377, A:Q.401 Water bridges: A:E.87, A:D.89, A:N.151, A:N.151, A:T.187, A:G.189, A:G.189, A:Y.325, A:Y.325, A:I.374 GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG.2: 27 residues within 4Å: Chain B: Y.85, V.86, D.88, D.90, F.93, F.95, Y.97, N.151, T.187, A.188, G.189, Y.201, H.203, F.216, S.217, H.218, Y.306, S.310, I.374, G.375, D.376, G.377, N.378, L.379, Q.401 Ligands: COA.7, MYR.12 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:D.88, B:F.93, B:F.93, B:F.95, B:F.95, B:F.216, B:F.216, B:I.374 Hydrogen bonds: B:Y.85, B:Y.85, B:T.187, B:F.216, B:I.374, B:D.376, B:D.376, B:D.376, B:G.377, B:G.377, B:Q.401 Water bridges: B:D.89, B:N.151, B:T.187, B:T.187, B:T.187, B:Y.201, B:H.203, B:Y.325, B:Q.401 Salt bridges: B:H.218

2 x COA: COENZYME A(Non-covalent)

COA.3: 23 residues within 4Å: Chain A: R.20, Y.22, Q.23, F.24, W.25, N.84, Y.85, V.86, L.153, C.154, V.155, R.160, S.161, K.162, R.163, V.164, A.165, P.166, T.187, A.188, L.192 Ligands: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG.1, MYR.11 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.85, A:V.86, A:L.153, A:V.155, A:A.165 Hydrogen bonds: A:R.20, A:R.20, A:Q.23, A:F.24, A:W.25, A:L.153, A:V.155, A:R.160, A:S.161, A:R.163, A:V.164, A:A.165 Water bridges: A:K.162, A:K.162 COA.7: 24 residues within 4Å: Chain B: R.20, Y.22, Q.23, F.24, W.25, N.84, Y.85, V.86, L.153, C.154, V.155, R.160, S.161, K.162, R.163, V.164, A.165, P.166, I.169, T.187, A.188, L.192 Ligands: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG.2, MYR.12 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.85, B:V.86, B:L.153, B:V.155 Hydrogen bonds: B:Q.23, B:F.24, B:W.25, B:L.153, B:V.155, B:R.160, B:S.161, B:R.163, B:V.164, B:A.165 Water bridges: B:K.162, B:K.162 Salt bridges: B:R.20

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 11 residues within 4Å: Chain A: P.31, K.194, P.195, V.196, Y.382, L.383, W.386, K.387, C.388, P.389, S.390 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.195, A:L.383, A:L.383, A:C.388, A:C.388 Water bridges: A:K.194 GOL.5: 8 residues within 4Å: Chain A: E.149, M.271, W.279, F.327, Y.328, V.399, L.400, Q.401 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.149, A:Y.328, A:Y.328, A:Q.401, A:Q.401 GOL.8: 10 residues within 4Å: Chain B: P.31, K.194, P.195, V.196, Y.382, L.383, W.386, K.387, C.388, S.390 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:P.195, B:L.383, B:L.383, B:C.388, B:C.388 Water bridges: B:K.194, B:S.390 GOL.9: 8 residues within 4Å: Chain B: E.149, P.269, M.271, W.279, Y.328, V.399, L.400, Q.401 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.328, B:Q.401, B:Q.401 Water bridges: B:E.149, B:W.279

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

CL.6: 6 residues within 4Å: Chain A: L.66, D.67, L.68, R.107, W.111, H.116 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: L.66, D.67, L.68, R.107, W.111, H.116 Ligand excluded by PLIP

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.11: 19 residues within 4Å: Chain A: W.25, Y.85, I.150, N.151, F.152, L.153, I.169, T.173, V.176, H.177, I.181, F.182, Q.183, A.184, Y.186, T.187, Y.384 Ligands: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG.1, COA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.150, A:I.150, A:L.153, A:I.169, A:V.176, A:A.184, A:Y.186, A:Y.186, A:Y.186, A:Y.186, A:Y.384 Hydrogen bonds: A:Y.85, A:F.152, A:L.153 MYR.12: 19 residues within 4Å: Chain B: W.25, Y.85, I.150, N.151, F.152, L.153, I.169, T.173, V.176, H.177, I.181, F.182, Q.183, A.184, Y.186, T.187, Y.384 Ligands: GLY-ASN-CYS-PHE-SER-LYS-ALA-ARG.2, COA.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.150, B:I.150, B:L.153, B:I.169, B:V.176, B:A.184, B:Y.186, B:Y.186, B:Y.186, B:Y.384 Hydrogen bonds: B:F.152, B:L.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dian, C. et al., HsNMT1 in complex with both MyrCoA and GNCFSKAR inhibitor peptide. to be published

Release Date

2024-08-14

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycylpeptide N-tetradecanoyltransferase 1

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