SMTL ID : 6f56.1

Mutant of Human N-myristoyltransferase with bound myristoyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

4 x MYA: TETRADECANOYL-COA(Non-covalent)

MYA.1: 34 residues within 4Å: Chain A: Y.31, Q.32, F.33, W.34, N.93, Y.94, V.95, I.159, N.160, F.161, L.162, C.163, V.164, R.169, S.170, K.171, R.172, V.173, A.174, P.175, I.178, T.182, V.185, H.186, I.190, F.191, Q.192, A.193, Y.195, T.196, A.197, L.201, Y.393 Ligands: MG.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34, A:Y.94, A:V.95, A:I.159, A:L.162, A:L.162, A:V.164, A:I.178, A:T.182, A:V.185, A:A.193, A:Y.195, A:Y.195, A:Y.195, A:Y.393 Hydrogen bonds: A:Q.32, A:F.33, A:W.34, A:Y.94, A:F.161, A:L.162, A:L.162, A:V.164, A:R.169, A:R.169, A:S.170, A:R.172, A:V.173, A:A.174 Salt bridges: A:R.172 MYA.5: 35 residues within 4Å: Chain B: R.29, Y.31, Q.32, F.33, W.34, N.93, Y.94, V.95, I.159, N.160, F.161, L.162, C.163, V.164, R.169, S.170, K.171, R.172, V.173, A.174, P.175, I.178, T.182, V.185, H.186, I.190, F.191, Q.192, A.193, Y.195, T.196, A.197, L.201, Y.393 Ligands: MG.6 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:W.34, B:W.34, B:Y.94, B:V.95, B:I.159, B:L.162, B:V.164, B:A.174, B:I.178, B:I.178, B:V.185, B:A.193, B:Y.195, B:Y.195, B:Y.393 Hydrogen bonds: B:Q.32, B:F.33, B:W.34, B:F.161, B:L.162, B:L.162, B:V.164, B:R.169, B:R.169, B:S.170, B:R.172, B:V.173, B:A.174 Water bridges: B:R.29, B:R.29 MYA.9: 33 residues within 4Å: Chain C: Y.31, Q.32, F.33, W.34, N.93, Y.94, V.95, I.159, N.160, F.161, L.162, C.163, V.164, R.169, S.170, K.171, R.172, V.173, A.174, P.175, I.178, T.182, V.185, I.190, F.191, Q.192, A.193, Y.195, T.196, A.197, L.201, Y.393 Ligands: MG.10 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:W.34, C:W.34, C:Y.94, C:V.95, C:I.159, C:I.159, C:L.162, C:L.162, C:V.164, C:A.174, C:I.178, C:V.185, C:A.193, C:Y.195, C:Y.195, C:Y.393 Hydrogen bonds: C:Q.32, C:F.33, C:W.34, C:Y.94, C:F.161, C:L.162, C:L.162, C:V.164, C:R.169, C:R.169, C:S.170, C:R.172, C:V.173, C:A.174 MYA.13: 34 residues within 4Å: Chain D: Y.31, Q.32, F.33, W.34, N.93, Y.94, V.95, I.159, N.160, F.161, L.162, C.163, V.164, R.169, S.170, K.171, R.172, V.173, A.174, P.175, I.178, T.182, V.185, H.186, I.190, F.191, Q.192, A.193, Y.195, T.196, A.197, L.201, Y.393 Ligands: MG.14 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:W.34, D:W.34, D:Y.94, D:V.95, D:I.159, D:I.159, D:L.162, D:L.162, D:L.162, D:V.164, D:I.178, D:V.185, D:Y.195, D:Y.393 Hydrogen bonds: D:Q.32, D:F.33, D:W.34, D:F.161, D:L.162, D:L.162, D:V.164, D:R.169, D:R.169, D:S.170, D:K.171, D:R.172, D:R.172, D:V.173, D:A.174

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: L.168, R.169, S.170, K.171, R.172, V.173 Ligands: MYA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:L.168 MG.6: 7 residues within 4Å: Chain B: L.168, R.169, S.170, K.171, R.172, V.173 Ligands: MYA.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:L.168 MG.10: 7 residues within 4Å: Chain C: L.168, R.169, S.170, K.171, R.172, V.173 Ligands: MYA.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:L.168 MG.14: 7 residues within 4Å: Chain D: L.168, R.169, S.170, K.171, R.172, V.173 Ligands: MYA.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:L.168

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: P.40, K.203, P.204, V.205, Y.391, L.392, W.395, K.396, C.397, P.398, S.399 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.204, A:L.392, A:L.392, A:W.395, A:C.397 GOL.4: 6 residues within 4Å: Chain A: E.158, W.288, F.336, Y.337, L.407, V.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.337, A:V.408 Water bridges: A:W.288 GOL.7: 10 residues within 4Å: Chain B: P.40, K.203, P.204, V.205, Y.391, L.392, W.395, K.396, C.397, S.399 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.204, B:L.392, B:L.392, B:W.395, B:C.397 Water bridges: B:K.203 GOL.8: 8 residues within 4Å: Chain B: E.158, P.278, M.280, W.288, F.336, Y.337, L.407, V.408 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.408 Water bridges: B:P.144, B:E.158 GOL.11: 8 residues within 4Å: Chain C: E.158, P.278, M.280, W.288, F.336, Y.337, L.407, V.408 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.337, C:Y.337 GOL.12: 10 residues within 4Å: Chain C: P.40, K.203, P.204, V.205, Y.391, L.392, W.395, K.396, C.397, S.399 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:P.204, C:V.205, C:L.392, C:L.392, C:W.395, C:C.397 GOL.15: 7 residues within 4Å: Chain D: E.158, P.278, W.288, F.336, Y.337, L.407, V.408 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.337, D:Y.337 GOL.16: 10 residues within 4Å: Chain D: P.40, K.203, P.204, V.205, Y.391, L.392, W.395, K.396, C.397, S.399 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:P.204, D:L.392, D:L.392, D:W.395, D:C.397 Water bridges: D:K.203 GOL.17: 5 residues within 4Å: Chain D: T.36, Q.37, E.53, K.56, R.179 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.36, D:Q.37, D:E.53, D:K.56, D:R.179, D:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kersten, C. et al., How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System. J.Med.Chem. (2019)

Release Date

2019-03-20

Peptides

Glycylpeptide N-tetradecanoyltransferase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycylpeptide N-tetradecanoyltransferase 1