SMTL ID : 9evj.1

Crystal Structure of human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: complex with Mn2+ and UDP-Gal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

GDU.1: 19 residues within 4Å: Chain A: 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, H.208, S.209, D.238, I.239, P.267 Ligands: CA.9 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:R.34, A:R.112, A:V.116 Hydrogen bonds: A:R.34, A:R.34, A:D.64, A:Y.99, A:R.112, A:R.120, A:D.139, A:A.140, A:S.209, A:D.238 Water bridges: A:D.64, A:D.64, A:K.106, A:K.106, A:W.108 Salt bridges: A:H.208 GDU.10: 19 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, H.208, S.209, D.238, I.239, P.267 Ligands: CA.15 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.112, B:V.116 Hydrogen bonds: B:R.34, B:R.34, B:D.64, B:R.112, B:R.120, B:D.139, B:A.140, B:S.209, B:D.238 Water bridges: B:R.34, B:D.64, B:K.106, B:K.106, B:K.106, B:L.268 Salt bridges: B:H.208

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 21 residues within 4Å: Chain A: I.319, N.320, L.321, R.327, A.347, V.348, D.349, G.350, G.381, G.384, C.385, S.388, E.408, D.409, D.410, Y.540, V.541, S.542, D.543, T.544 Ligands: MN.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.321 Hydrogen bonds: A:L.321, A:V.348, A:V.348, A:G.350, A:C.385, A:S.388, A:D.409, A:D.409, A:D.543, A:T.544, A:T.544 Salt bridges: A:R.327

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 2 residues within 4Å: Chain A: D.410 Ligands: UDP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.410

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

MES.4: 7 residues within 4Å: Chain A: E.103, G.104, P.105, H.271, S.272, T.273, L.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.274 Water bridges: A:Q.275 MES.5: 6 residues within 4Å: Chain A: L.268, S.272, D.276, F.416, R.419, R.420 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.276, A:R.419

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: H.271 Ligands: CL.13, NA.14 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: H.271 Ligands: CL.13, NA.14 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Ligands: CL.11, CL.12, NA.14 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 2 residues within 4Å: Chain A: D.141 Ligands: GDU.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.141, A:D.141, H2O.1, H2O.2, H2O.2 CA.15: 2 residues within 4Å: Chain B: D.141 Ligands: GDU.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.141, H2O.3, H2O.5

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

NA.14: 4 residues within 4Å: Chain B: H.271 Ligands: CL.11, CL.12, CL.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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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