SMTL ID : 6i7s.1 (1 other biounit)

Microsomal triglyceride transfer protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: A.365, D.367, K.370, F.430, P.431 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.365, A:D.367, A:K.370, A:F.430, A:P.431

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: K.146, S.174, D.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.183 EDO.3: 7 residues within 4Å: Chain A: V.134, S.137, E.138, F.190, K.191, K.192, G.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.190, A:K.191 EDO.4: 2 residues within 4Å: Chain A: V.221, K.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.221, A:K.260 EDO.5: 1 residues within 4Å: Chain A: K.399 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: F.330, G.333 No protein-ligand interaction detected (PLIP) EDO.17: 1 residues within 4Å: Chain B: R.613 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.613 Water bridges: B:R.613, B:R.613 EDO.18: 1 residues within 4Å: Chain B: R.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.111, B:R.111 EDO.19: 3 residues within 4Å: Chain B: N.130, E.131, A.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.130 EDO.20: 3 residues within 4Å: Chain B: Q.285, S.286, K.738 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.286, B:K.738 EDO.21: 2 residues within 4Å: Chain B: R.302, N.342 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.302, B:R.302, B:N.342 EDO.22: 8 residues within 4Å: Chain B: S.355, Q.357, A.386, F.389, A.390, S.391, I.722, L.723 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.391, B:S.391, B:L.723 Water bridges: B:L.721

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.7: 7 residues within 4Å: Chain B: S.636, L.638, S.652, V.654, N.770, A.799, F.803 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.636, B:S.652, B:N.770

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 6 residues within 4Å: Chain B: E.381, Y.385, L.691, V.694, V.718, G.720 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.692 Water bridges: B:L.721

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

TRS.9: 5 residues within 4Å: Chain B: L.16, Y.24, L.26, V.217, L.248 No protein-ligand interaction detected (PLIP)

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain B: G.840, R.841, G.842 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.841, B:G.842 SO4.11: 3 residues within 4Å: Chain B: E.80, N.81, F.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.81, B:S.90 Water bridges: B:N.81, B:Q.84 SO4.12: 4 residues within 4Å: Chain B: E.526, K.527, T.528, R.634 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.526, B:K.527, B:T.528 Salt bridges: B:R.634 SO4.13: 3 residues within 4Å: Chain B: S.29, R.48, K.245 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.29, B:S.29 Water bridges: B:T.27 Salt bridges: B:R.48, B:K.245 SO4.14: 4 residues within 4Å: Chain B: F.757, S.758, L.759, W.760 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.758, B:L.759, B:W.760 SO4.15: 4 residues within 4Å: Chain A: R.284 Chain B: Q.559, R.600, S.601 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.559, B:S.601 Water bridges: B:N.562, B:N.562 Salt bridges: B:R.600, A:R.284 SO4.16: 3 residues within 4Å: Chain B: T.167, I.178, A.180 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.167

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.23: 3 residues within 4Å: Chain B: G.631, I.632, L.633 No protein-ligand interaction detected (PLIP) PEG.24: 6 residues within 4Å: Chain B: Q.499, R.500, N.539, F.641, H.650, Q.653 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.639, B:Q.653

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biterova, E.I. et al., The crystal structure of human microsomal triglyceride transfer protein. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-08-21

Peptides

Protein disulfide-isomerase: A
Microsomal triglyceride transfer protein large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

Protein disulfide-isomerase

Microsomal triglyceride transfer protein large subunit

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