SMTL ID : 9evk.1

Crystal Structure of human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: H.271 Ligands: NA.8, CL.11 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: H.271 Ligands: NA.8, CL.11 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Ligands: NA.8, CL.9, CL.10 Ligand excluded by PLIP

2 x GDU: GALACTOSE-URIDINE-5'-DIPHOSPHATE(Non-covalent)

GDU.4: 20 residues within 4Å: Chain A: L.32, A.33, R.34, D.64, H.65, Y.99, W.108, R.112, Y.113, V.116, R.120, D.139, A.140, D.141, H.208, S.209, D.238, I.239, P.267 Ligands: CA.7 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.112, A:V.116 Hydrogen bonds: A:R.34, A:R.34, A:R.34, A:D.64, A:H.65, A:Y.99, A:R.112, A:R.120, A:R.120, A:D.139, A:A.140, A:S.209, A:D.238 Water bridges: A:D.64, A:D.64 Salt bridges: A:H.208 GDU.12: 18 residues within 4Å: Chain B: L.32, A.33, R.34, D.64, Y.99, W.108, R.112, Y.113, V.116, R.120, D.139, A.140, D.141, S.209, D.238, I.239, P.267 Ligands: CA.13 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:R.34, B:V.116 Hydrogen bonds: B:R.34, B:R.34, B:D.64, B:R.112, B:Y.113, B:Y.113, B:R.120, B:D.139, B:D.139, B:A.140, B:S.209, B:D.238 Salt bridges: B:H.208

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 7 residues within 4Å: Chain A: E.103, G.104, P.105, H.271, S.272, T.273, L.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.274 MES.6: 5 residues within 4Å: Chain A: L.268, S.272, D.276, F.416, R.419 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.276, A:R.419

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain A: D.141 Ligands: GDU.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.141, A:D.141 CA.13: 2 residues within 4Å: Chain B: D.141 Ligands: GDU.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.141, B:D.141

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain B: H.271 Ligands: CL.9, CL.10, CL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.271, B:H.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Marco, M. et al., Molecular structure and enzymatic mechanism of the human collagen hydroxylysine galactosyltransferase GLT25D1/COLGALT1. Nat Commun (2025)

Release Date

2025-04-09

Peptides

Procollagen galactosyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Procollagen galactosyltransferase 1

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