B1MDI3 | AlphaKnot 2.0

AF4

Categories voted by users:

Information

Protein name	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) (M1G-methyltransferase) (tRNA [GM37] methyltransferase)
Main knot	3₁ (86%)
Global pLDDT	93.09
Species	Mycobacterium abscessus
UniProt	B1MDI3
Structure Prediction Model	AlphaFold v4: B1MDI3
PDB structures	3QUV A/B 6NVR A/B 6NW6 A/B 6NW7 A/B 6QO2 A/B 6QO3 A/B 6QO4 A/B 6QO6 A/B 6QOA A/B 6QOC A/B 6QOD A/B 6QOE A/B 6QOF A/B 6QOG A/B 6QOH A/B 6QOI A/B 6QOJ A/B 6QOK A/B 6QOL A/B 6QOM A/B 6QON A/B 6QOO A/B 6QOP A/B 6QOQ A/B 6QOR A/B 6QOS A/B 6QOT A/B 6QOU A/B 6QOV A/B 6QOW A/B 6QOX A/B 6QQQ A/B 6QQR A/B 6QQS A/B 6QQT A/B 6QQU A/B 6QQV A/B 6QQW A/B 6QQX A/B 6QQY A/B 6QQZ A/B 6QR0 A/B 6QR1 A/B 6QR2 A/B 6QR3 A/B 6QR4 A/B 6QR5 A/B 6QR6 A/B 6QR7 A/B 6QR8 A/B 6QR9 A/B 6QRA A/B 6QRB A/B 6QRC A/B 6QRD A/B 6QRE A/B 6QRF A/B 6QRG A/B
Structures in KnotProt	3QUV A/B, K +3.1: 1-242 6QQQ A/B, K +3.1: 1-242 6QQR A/B, K +3.1: 1-242 6QQT A/B, K +3.1: 1-242 6QQV A/B, K +3.1: 1-242 6QQW A/B, K +3.1: 1-242 6QQZ A/B, K +3.1: 1-242 6QR0 A/B, K +3.1: 1-242 6QR1 A/B, K +3.1: 1-242 6QR2 A/B, K +3.1: 1-242 6QR3 A/B, K +3.1: 1-242 6QRA A/B, K +3.1: 1-242 6QRC A/B, K +3.1: 1-242 6QRD A/B, K +3.1: 1-242 6QRE A/B, K +3.1: 1-242 6QRF A/B, K +3.1: 1-242 6QRG A/B, K +3.1: 1-242
Model length	242
AlphaFold deposition date	2022-06-01
AlphaKnot deposition date	2023-01-27

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Knot types & Model sequence

					Knot pLDDT	Knot core range	Knot core length	Knot tails range	N-end length	C-end length	Main Knot
					98.0	80-131	52	1-79, 132-242	79	111

Model Sequence

MKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVLGNALSAQEDSHSEGMASLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLLGFDSPTGEHGGDGLS

Comments

ESM1

Categories voted by users:

Information

Protein name	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) (M1G-methyltransferase) (tRNA [GM37] methyltransferase)
Main knot	3₁ (82%)
Global pLDDT	92.51
Species	Mycobacterium abscessus
UniProt	B1MDI3
Structure Prediction Model	ESM v1: esmfold_v1 - nov. 2022
PDB structures	3QUV A/B 6NVR A/B 6NW6 A/B 6NW7 A/B 6QO2 A/B 6QO3 A/B 6QO4 A/B 6QO6 A/B 6QOA A/B 6QOC A/B 6QOD A/B 6QOE A/B 6QOF A/B 6QOG A/B 6QOH A/B 6QOI A/B 6QOJ A/B 6QOK A/B 6QOL A/B 6QOM A/B 6QON A/B 6QOO A/B 6QOP A/B 6QOQ A/B 6QOR A/B 6QOS A/B 6QOT A/B 6QOU A/B 6QOV A/B 6QOW A/B 6QOX A/B 6QQQ A/B 6QQR A/B 6QQS A/B 6QQT A/B 6QQU A/B 6QQV A/B 6QQW A/B 6QQX A/B 6QQY A/B 6QQZ A/B 6QR0 A/B 6QR1 A/B 6QR2 A/B 6QR3 A/B 6QR4 A/B 6QR5 A/B 6QR6 A/B 6QR7 A/B 6QR8 A/B 6QR9 A/B 6QRA A/B 6QRB A/B 6QRC A/B 6QRD A/B 6QRE A/B 6QRF A/B 6QRG A/B
Structures in KnotProt	3QUV A/B, K +3.1: 1-242 6QQQ A/B, K +3.1: 1-242 6QQR A/B, K +3.1: 1-242 6QQT A/B, K +3.1: 1-242 6QQV A/B, K +3.1: 1-242 6QQW A/B, K +3.1: 1-242 6QQZ A/B, K +3.1: 1-242 6QR0 A/B, K +3.1: 1-242 6QR1 A/B, K +3.1: 1-242 6QR2 A/B, K +3.1: 1-242 6QR3 A/B, K +3.1: 1-242 6QRA A/B, K +3.1: 1-242 6QRC A/B, K +3.1: 1-242 6QRD A/B, K +3.1: 1-242 6QRE A/B, K +3.1: 1-242 6QRF A/B, K +3.1: 1-242 6QRG A/B, K +3.1: 1-242
Model length	242
ESM generation time	2023-06-24: download the generated 3D model
AlphaKnot deposition date	2023-06-28

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Knot types & Model sequence

					Knot pLDDT	Knot core range	Knot core length	Knot tails range	N-end length	C-end length	Main Knot
					91.6	82-131	50	1-81, 132-242	81	111

Model Sequence

Comments

Domain	Bacteria
Family	Mycobacteriaceae
Species (Full Name)	Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (Mycobacterium abscessus)
Gene	trmD MAB_3226c
PFAM codes	PF01746
InterPro codes	IPR002649, IPR016009, IPR023148, IPR029026, IPR029028
PDB structures (whole Protein)	3QUV A/B: 1-242 6NVR A/B: 1-242 6NW6 A/B: 1-242 6NW7 A/B: 1-242 6QO2 A/B: 1-242 6QO3 A/B: 1-242 6QO4 A/B: 1-242 6QO6 A/B: 1-242 6QOA A/B: 1-242 6QOC A/B: 1-242 6QOD A/B: 1-242 6QOE A/B: 1-242 6QOF A/B: 1-242 6QOG A/B: 1-242 6QOH A/B: 1-242 6QOI A/B: 1-242 6QOJ A/B: 1-242 6QOK A/B: 1-242 6QOL A/B: 1-242 6QOM A/B: 1-242 6QON A/B: 1-242 6QOO A/B: 1-242 6QOP A/B: 1-242 6QOQ A/B: 1-242 6QOR A/B: 1-242 6QOS A/B: 1-242 6QOT A/B: 1-242 6QOU A/B: 1-242 6QOV A/B: 1-242 6QOW A/B: 1-242 6QOX A/B: 1-242 6QQQ A/B: 1-242 6QQR A/B: 1-242 6QQS A/B: 1-242 6QQT A/B: 1-242 6QQU A/B: 1-242 6QQV A/B: 1-242 6QQW A/B: 1-242 6QQX A/B: 1-242 6QQY A/B: 1-242 6QQZ A/B: 1-242 6QR0 A/B: 1-242 6QR1 A/B: 1-242 6QR2 A/B: 1-242 6QR3 A/B: 1-242 6QR4 A/B: 1-242 6QR5 A/B: 1-242 6QR6 A/B: 1-242 6QR7 A/B: 1-242 6QR8 A/B: 1-242 6QR9 A/B: 1-242 6QRA A/B: 1-242 6QRB A/B: 1-242 6QRC A/B: 1-242 6QRD A/B: 1-242 6QRE A/B: 1-242 6QRF A/B: 1-242 6QRG A/B: 1-242

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similar chains with experimentally solved models (PDB) in the AlphaKnot 2.0 database (?% sequence similarity)

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similar chains with experimentally solved models not found in AlphaKnot 2.0 database but found in thePDB database (?% sequence similarity)

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B1MDI3F1

AF4

Model Sequence

ESM1

Model Sequence