SMTL ID : 8ic1.1 (1 other biounit)

endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x BXY- BXY- BXY- BXY: alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose

BXY-BXY-BXY-BXY.1: 10 residues within 4Å: Chain A: N.361, D.365, F.379, R.381, Y.382, N.383, D.466, W.468, Q.470 Ligands: PEG.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.365, A:R.381, A:Q.470 Water bridges: A:R.381

2 x BXY- BXY- BXY: alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose

BXY-BXY-BXY.2: 16 residues within 4Å: Chain A: D.33, G.50, N.51, I.117, W.138, P.141, G.142, W.144, R.198, L.260, A.291, L.292, Y.293, W.313, Y.316 Ligands: OYO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.198 Water bridges: A:A.291 BXY-BXY-BXY.3: 16 residues within 4Å: Chain B: D.33, G.50, N.51, I.117, W.138, P.141, G.142, W.144, R.198, L.260, A.291, L.292, Y.293, W.313, Y.316 Ligands: OYO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.198 Water bridges: B:P.141, B:A.291

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: M.37, W.182, V.183, V.246, Q.247, F.297, H.298, P.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.121, A:V.246, A:Q.247 Water bridges: A:S.245 GOL.10: 7 residues within 4Å: Chain A: I.104, P.105, K.107, E.113, T.116, F.148, V.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.113 GOL.12: 8 residues within 4Å: Chain B: M.37, G.121, W.182, V.183, V.246, Q.247, F.297, P.299 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.246, B:Q.247, B:F.297 Water bridges: B:S.245 GOL.14: 5 residues within 4Å: Chain B: N.361, R.381, Y.382, N.383, D.466 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.361 GOL.15: 4 residues within 4Å: Chain B: D.365, F.379, R.381, Q.470 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.381, B:R.381, B:Q.470 Water bridges: B:D.365 GOL.20: 8 residues within 4Å: Chain B: I.104, P.105, K.107, E.113, T.116, F.132, F.148, V.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.113 GOL.22: 4 residues within 4Å: Chain B: D.365, N.366, A.367, R.377 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.366, B:R.377 Water bridges: B:D.365

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

PGE.5: 6 residues within 4Å: Chain A: K.136, Q.137, D.145, T.146, N.147, N.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.136, A:Q.137 Water bridges: A:G.111 PGE.6: 4 residues within 4Å: Chain A: Y.251, S.252, K.253, R.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.253, A:R.327 Water bridges: A:R.327 PGE.13: 7 residues within 4Å: Chain B: K.136, Q.137, D.145, T.146, N.147, N.170, G.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.136, B:Q.137 Water bridges: B:D.145

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

PEG.7: 5 residues within 4Å: Chain A: R.381, N.412, D.466, W.468 Ligands: BXY-BXY-BXY-BXY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.412 PEG.17: 5 residues within 4Å: Chain B: K.185, T.188, Y.190, F.255 Ligands: MES.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.188, B:T.188, B:T.271

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

NA.8: 4 residues within 4Å: Chain A: D.80, D.82, D.85, G.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.82, A:D.82 NA.18: 4 residues within 4Å: Chain B: D.80, D.82, D.85, G.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.86

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: S.341, E.343, T.373, H.376, D.472 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.341, A:S.341, A:E.343, A:T.373, A:H.376 CA.19: 5 residues within 4Å: Chain B: S.341, E.343, T.373, H.376, D.472 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.341, B:S.341, B:E.343, B:T.373, B:H.376

2 x OYO: (3~{a}~{S},5~{R},6~{R},6~{a}~{S})-5-(hydroxymethyl)-2,2-dimethyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]dioxol-6-ol(Non-covalent)

OYO.11: 9 residues within 4Å: Chain A: N.51, F.53, G.62, G.63, W.138, W.313, Y.316 Ligands: BXY-BXY-BXY.2, BXY-BXY-BXY.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.138, A:W.138 Hydrogen bonds: A:N.51, A:Y.316 OYO.21: 8 residues within 4Å: Chain B: N.51, F.53, G.62, G.63, W.138, W.313, Y.316 Ligands: BXY-BXY-BXY.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.138, B:W.138 Hydrogen bonds: B:N.51

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

MES.16: 4 residues within 4Å: Chain B: T.188, Y.190, K.206 Ligands: PEG.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.188, B:Y.190 Salt bridges: B:K.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimokawa, M. et al., Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria. Nat Commun (2023)

Release Date

2023-08-16

Peptides

endo-alpha-D-arabinanase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

endo-alpha-D-arabinanase

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