SMTL ID : 9evl.1

Crystal Structure of human Collagen Hydroxylysine Galactosyltransferase GLT25D1/COLGALT1: Hg2+ soak for experimental phasing

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

9 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 4 residues within 4Å: Chain A: F.242, A.243, C.246, M.253 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.246 HG.2: 2 residues within 4Å: Chain A: C.176, I.193 No protein-ligand interaction detected (PLIP) HG.3: 3 residues within 4Å: Chain A: C.385, E.408, T.469 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.385, A:E.408 HG.4: 5 residues within 4Å: Chain A: H.283, E.287, R.412, F.413, E.414 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.283 HG.5: 3 residues within 4Å: Chain A: L.332, C.342 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.342, A:C.342 HG.14: 4 residues within 4Å: Chain B: F.242, A.243, C.246, M.253 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.246 HG.15: 2 residues within 4Å: Chain B: C.176, I.193 No protein-ligand interaction detected (PLIP) HG.16: 3 residues within 4Å: Chain B: L.332, C.342 Ligands: CL.20 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.342 HG.17: 3 residues within 4Å: Chain B: H.271 Ligands: CL.18, CL.19 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.271

7 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.9: 3 residues within 4Å: Chain A: L.335, I.340 Ligands: HG.5 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Ligands: HG.17 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: H.271 Ligands: HG.17 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: I.340, E.341, C.342 Ligands: HG.16 Ligand excluded by PLIP

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

GDU.10: 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.13 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.34, A:R.112, A:V.116 Hydrogen bonds: A:R.34, A:R.34, A:R.34, A:D.64, A:R.112, A:R.120, A:R.120, A:D.139, A:A.140, A:D.238 Water bridges: A:D.64, A:D.64, A:D.139, A:D.139 Salt bridges: A:H.208 GDU.21: 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.22 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.34, B:R.112, B:V.116 Hydrogen bonds: B:R.34, B:R.34, B:R.34, B:D.64, B:Y.99, B:W.108, B:R.112, B:R.120, B:D.139, B:A.140, B:S.209, B:D.238 Water bridges: B:D.64

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

MES.11: 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.12: 7 residues within 4Å: Chain A: L.268, S.272, D.276, F.416, R.419, R.420, N.423 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.423 Salt bridges: A:D.276, A:R.419

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 2 residues within 4Å: Chain A: D.141 Ligands: GDU.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.141, A:D.141 CA.22: 2 residues within 4Å: Chain B: D.141 Ligands: GDU.21 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.141, B:D.141

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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