SMTL ID : 7d72.1

Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-Mannose

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-4-mer

Ligands

12 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)(Covalent)

GDD.1: 18 residues within 4Å: Chain A: L.6, V.7, G.8, A.52, E.80, G.85, T.86, P.89, N.108, S.109, D.110, Y.144, G.145, N.172, Y.176, E.194, W.216, D.218 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.7, A:G.8, A:S.109, A:S.109, A:D.110, A:D.110, A:G.145, A:N.172, A:N.172, A:E.194, A:E.194 Salt bridges: A:E.80 GDD.2: 16 residues within 4Å: Chain B: L.6, V.7, G.8, A.52, G.85, P.89, N.108, S.109, D.110, Y.144, G.145, E.161, N.172, E.194, W.216, D.218 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:V.7, B:E.80, B:S.109, B:D.110, B:G.145, B:E.161, B:N.172, B:N.172, B:Y.176, B:E.194, B:D.218 GDD.3: 24 residues within 4Å: Chain C: L.7, I.8, G.9, K.13, I.56, F.58, E.85, G.90, N.114, A.115, D.116, V.117, Y.152, G.153, Y.167, E.169, K.170, N.180, C.181, Y.184, E.223, W.245, Q.247, K.249 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:I.56, C:G.90, C:N.114, C:A.115, C:D.116, C:G.153, C:E.169, C:N.180, C:N.180, C:C.181, C:E.223 Salt bridges: C:E.85, C:K.170, C:K.170, C:K.170, C:K.249, C:K.249 GDD.4: 25 residues within 4Å: Chain D: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, L.89, G.90, N.114, A.115, D.116, V.117, Y.152, G.153, Y.167, E.169, K.170, N.180, Y.184, E.223, W.245, Q.247, K.249 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:I.56, D:L.89, D:G.90, D:N.114, D:A.115, D:D.116, D:G.153, D:Y.167, D:E.169, D:N.180, D:N.180, D:Y.184, D:E.223, D:E.223 Salt bridges: D:E.85, D:K.170, D:K.170, D:K.249, D:K.249 GDD.5: 24 residues within 4Å: Chain E: L.7, I.8, G.9, K.13, I.56, G.57, F.58, E.85, G.90, N.114, A.115, D.116, V.117, Y.152, G.153, Y.167, E.169, K.170, N.180, Y.184, E.223, W.245, Q.247, K.249 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:I.56, E:G.90, E:N.114, E:A.115, E:D.116, E:G.153, E:E.169, E:N.180, E:N.180, E:Y.184, E:E.223 Salt bridges: E:E.85, E:K.170, E:K.249, E:K.249 GDD.6: 25 residues within 4Å: Chain F: L.7, I.8, G.9, K.13, I.56, F.58, E.85, G.90, T.91, N.114, A.115, D.116, V.117, Y.152, G.153, Y.167, E.169, K.170, N.180, C.181, Y.184, E.223, W.245, Q.247, K.249 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:I.56, F:L.89, F:G.90, F:N.114, F:A.115, F:D.116, F:G.153, F:Y.167, F:E.169, F:N.180, F:N.180, F:E.223 Salt bridges: F:E.85, F:K.170, F:K.170, F:K.249, F:K.249 GDD.7: 21 residues within 4Å: Chain G: L.6, V.7, G.8, K.23, A.52, S.54, E.80, P.83, G.85, T.86, N.108, S.109, D.110, V.111, Y.144, G.145, N.172, Y.176, E.194, D.218 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:V.7, G:V.7, G:S.54, G:S.54, G:G.85, G:T.86, G:N.108, G:S.109, G:S.109, G:D.110, G:G.145, G:N.172, G:N.172, G:E.194, G:D.218 Salt bridges: G:K.23, G:E.80 GDD.9: 23 residues within 4Å: Chain H: L.6, V.7, G.8, K.23, A.52, S.54, P.83, G.85, T.86, P.89, N.108, S.109, D.110, V.111, Y.144, G.145, E.161, K.162, N.172, Y.176, E.194, D.218 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:V.7, H:A.52, H:S.54, H:S.54, H:G.85, H:S.109, H:S.109, H:D.110, H:G.145, H:N.172, H:N.172, H:E.194, H:E.194 Salt bridges: H:K.23, H:E.80, H:K.162, H:K.162 GDD.11: 20 residues within 4Å: Chain I: L.6, V.7, G.8, A.52, E.80, G.85, P.89, N.108, S.109, D.110, V.111, Y.144, G.145, E.161, N.172, Y.176, E.194, W.216, D.218 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:V.7, I:A.52, I:G.85, I:T.86, I:S.109, I:S.109, I:D.110, I:D.110, I:G.145, I:E.161, I:N.172, I:N.172, I:Y.176, I:E.194 Salt bridges: I:E.80 GDD.13: 18 residues within 4Å: Chain J: L.6, V.7, G.8, Y.10, S.54, E.80, G.85, P.89, N.108, S.109, D.110, Y.144, G.145, N.172, Y.176, E.194, W.216, D.218 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:G.8, J:Y.10, J:S.54, J:S.54, J:G.85, J:S.109, J:D.110, J:G.145, J:N.172, J:N.172, J:E.194 Salt bridges: J:E.80 GDD.14: 18 residues within 4Å: Chain K: L.6, V.7, G.8, R.13, E.80, G.85, P.89, N.108, S.109, D.110, V.111, Y.144, G.145, N.172, Y.176, E.194, W.216, D.218 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:V.7, K:G.8, K:G.8, K:G.85, K:S.109, K:S.109, K:S.109, K:D.110, K:G.145, K:N.172, K:N.172, K:E.194 Salt bridges: K:R.13, K:E.80 GDD.15: 20 residues within 4Å: Chain L: L.6, V.7, G.8, K.23, A.52, E.80, G.85, T.86, N.108, S.109, D.110, V.111, Y.144, G.145, E.161, K.162, N.172, Y.176, E.194, W.216 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:V.7, L:G.8, L:G.8, L:G.85, L:S.109, L:D.110, L:G.145, L:E.161, L:E.161, L:N.172, L:N.172, L:E.194 Salt bridges: L:K.23, L:E.80, L:K.162, L:K.162

3 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain G: K.23, D.110, D.218 Ligands: GDD.7 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.110, G:D.218, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain H: K.23, D.110, D.218 Ligands: GDD.9 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.110, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain I: D.110, D.218, G.220 Ligands: GDD.11 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.218, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, L. et al., Cryo-EM structures of human GMPPA-GMPPB complex reveal how cells maintain GDP-mannose homeostasis. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-05-05

Peptides

Mannose-1-phosphate guanyltransferase beta: ABGHIJKL
Mannose-1-phosphate guanyltransferase alpha: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
I

G
E

H
F

I
G

J
H

K
J

L
L

C
A

D
B

E
C

F
D

Mannose-1-phosphate guanyltransferase beta

Mannose-1-phosphate guanyltransferase alpha

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